Starting phenix.real_space_refine on Mon Aug 25 07:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5q_38072/08_2025/8x5q_38072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5q_38072/08_2025/8x5q_38072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5q_38072/08_2025/8x5q_38072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5q_38072/08_2025/8x5q_38072.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5q_38072/08_2025/8x5q_38072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5q_38072/08_2025/8x5q_38072.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.066 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 111 5.16 5 C 16689 2.51 5 N 4278 2.21 5 O 5130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26208 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.13, per 1000 atoms: 0.27 Number of scatterers: 26208 At special positions: 0 Unit cell: (150, 140, 167, 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 111 16.00 O 5130 8.00 N 4278 7.00 C 16689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 616 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 616 " " NAG D 1 " - " ASN C 122 " " NAG E 1 " - " ASN C 165 " " NAG F 1 " - " ASN C 234 " " NAG G 1 " - " ASN C 343 " " NAG H 1 " - " ASN C 354 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN C1134 " " NAG K 1 " - " ASN A 122 " " NAG L 1 " - " ASN A 165 " " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 343 " " NAG O 1 " - " ASN A 354 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 165 " " NAG T 1 " - " ASN B 234 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 354 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 51 sheets defined 21.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.712A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.660A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 869 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.299A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.605A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.782A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.694A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.646A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 869 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.586A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 941 removed outlier: 4.460A pdb=" N VAL A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.584A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.016A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.722A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.579A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.535A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 941 removed outlier: 4.466A pdb=" N VAL B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.593A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.339A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.643A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.603A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.603A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.571A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.259A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 317 removed outlier: 7.200A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.666A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.666A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.240A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.302A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.430A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.572A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.545A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'C' and resid 719 through 727 removed outlier: 7.606A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AB9, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AC2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'A' and resid 26 through 30 removed outlier: 3.676A pdb=" N SER A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.070A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.250A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.221A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.621A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.621A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.166A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.384A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 452 through 454 removed outlier: 4.334A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.574A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.566A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD7, first strand: chain 'A' and resid 719 through 727 removed outlier: 7.573A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AD9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'B' and resid 26 through 30 removed outlier: 3.660A pdb=" N SER B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.083A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.114A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.526A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.143A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.052A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.336A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.437A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'B' and resid 719 through 727 removed outlier: 7.332A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AF5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AF6, first strand: chain 'B' and resid 1094 through 1097 826 hydrogen bonds defined for protein. 2238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.82 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8085 1.34 - 1.46: 6456 1.46 - 1.59: 12135 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 26814 Sorted by residual: bond pdb=" N VAL C 70 " pdb=" CA VAL C 70 " ideal model delta sigma weight residual 1.456 1.494 -0.037 9.50e-03 1.11e+04 1.53e+01 bond pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.52e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.41e+01 bond pdb=" N GLY B 566 " pdb=" CA GLY B 566 " ideal model delta sigma weight residual 1.444 1.479 -0.035 1.02e-02 9.61e+03 1.21e+01 bond pdb=" N PHE C 140 " pdb=" CA PHE C 140 " ideal model delta sigma weight residual 1.458 1.488 -0.030 9.00e-03 1.23e+04 1.14e+01 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 34294 1.64 - 3.28: 1962 3.28 - 4.92: 223 4.92 - 6.56: 35 6.56 - 8.20: 11 Bond angle restraints: 36525 Sorted by residual: angle pdb=" N THR C 604 " pdb=" CA THR C 604 " pdb=" C THR C 604 " ideal model delta sigma weight residual 114.62 108.61 6.01 1.14e+00 7.69e-01 2.77e+01 angle pdb=" N THR B 604 " pdb=" CA THR B 604 " pdb=" C THR B 604 " ideal model delta sigma weight residual 114.62 108.62 6.00 1.14e+00 7.69e-01 2.77e+01 angle pdb=" N GLN A 628 " pdb=" CA GLN A 628 " pdb=" C GLN A 628 " ideal model delta sigma weight residual 114.56 107.96 6.60 1.27e+00 6.20e-01 2.70e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 114.62 108.72 5.90 1.14e+00 7.69e-01 2.68e+01 angle pdb=" C PHE C 32 " pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " ideal model delta sigma weight residual 116.54 111.06 5.48 1.15e+00 7.56e-01 2.27e+01 ... (remaining 36520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 14934 22.60 - 45.20: 1395 45.20 - 67.80: 233 67.80 - 90.40: 89 90.40 - 113.00: 122 Dihedral angle restraints: 16773 sinusoidal: 7287 harmonic: 9486 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 31.10 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 31.10 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 32.10 60.90 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 16770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3886 0.092 - 0.184: 413 0.184 - 0.276: 27 0.276 - 0.368: 4 0.368 - 0.460: 2 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.36e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 354 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 4329 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.254 2.00e-02 2.50e+03 2.12e-01 5.62e+02 pdb=" C7 NAG B1307 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.355 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.101 2.00e-02 2.50e+03 8.38e-02 8.77e+01 pdb=" C7 NAG A1306 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.134 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 190 " 0.741 9.50e-02 1.11e+02 3.32e-01 6.71e+01 pdb=" NE ARG A 190 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 190 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 190 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 190 " 0.022 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2155 2.74 - 3.28: 27214 3.28 - 3.82: 44072 3.82 - 4.36: 51547 4.36 - 4.90: 88873 Nonbonded interactions: 213861 Sorted by model distance: nonbonded pdb=" NH2 ARG B 34 " pdb=" O PRO B 217 " model vdw 2.198 3.120 nonbonded pdb=" O VAL C 608 " pdb=" OH TYR C 636 " model vdw 2.201 3.040 nonbonded pdb=" O VAL B 608 " pdb=" OH TYR B 636 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN B 804 " pdb=" OE1 GLN B 935 " model vdw 2.207 3.120 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.207 3.040 ... (remaining 213856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.020 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.006 0.078 26913 Z= 0.355 Angle : 0.830 13.408 36786 Z= 0.493 Chirality : 0.054 0.460 4332 Planarity : 0.009 0.332 4650 Dihedral : 20.555 112.997 10569 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.15 % Favored : 90.41 % Rotamer: Outliers : 1.21 % Allowed : 22.41 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.14), residues: 3234 helix: 1.01 (0.21), residues: 624 sheet: -0.77 (0.20), residues: 636 loop : -2.14 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.035 0.002 TYR A 655 PHE 0.047 0.001 PHE C 643 TRP 0.030 0.002 TRP C 633 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00560 (26814) covalent geometry : angle 0.80117 (36525) SS BOND : bond 0.00506 ( 36) SS BOND : angle 1.54772 ( 72) hydrogen bonds : bond 0.20197 ( 816) hydrogen bonds : angle 7.80781 ( 2238) link_BETA1-4 : bond 0.01009 ( 21) link_BETA1-4 : angle 4.16714 ( 63) link_NAG-ASN : bond 0.00377 ( 42) link_NAG-ASN : angle 2.19786 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 ASN cc_start: 0.7038 (t0) cc_final: 0.6274 (p0) REVERT: C 141 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4313 (tt) REVERT: C 298 GLU cc_start: 0.8718 (tp30) cc_final: 0.8517 (tp30) REVERT: C 457 ARG cc_start: 0.6180 (mtp-110) cc_final: 0.5693 (mtp-110) REVERT: A 141 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6187 (mt) REVERT: A 655 TYR cc_start: 0.8361 (t80) cc_final: 0.8026 (t80) REVERT: B 582 LEU cc_start: 0.8435 (mp) cc_final: 0.8206 (pp) outliers start: 34 outliers final: 14 residues processed: 291 average time/residue: 0.1612 time to fit residues: 76.5781 Evaluate side-chains 225 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 580 GLN C 613 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 955 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1125 ASN A 69 HIS A 321 GLN A 580 GLN A 613 GLN A 804 GLN A 895 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 580 GLN B 804 GLN B 955 ASN B1005 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.127577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097737 restraints weight = 50727.984| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.08 r_work: 0.3241 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26913 Z= 0.182 Angle : 0.766 22.693 36786 Z= 0.362 Chirality : 0.050 0.421 4332 Planarity : 0.004 0.072 4650 Dihedral : 15.360 98.283 4839 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.26 % Favored : 91.50 % Rotamer: Outliers : 3.65 % Allowed : 21.06 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.14), residues: 3234 helix: 1.15 (0.21), residues: 609 sheet: -0.59 (0.19), residues: 654 loop : -2.03 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 102 TYR 0.023 0.002 TYR A1067 PHE 0.022 0.001 PHE C 168 TRP 0.021 0.002 TRP A 353 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00417 (26814) covalent geometry : angle 0.71720 (36525) SS BOND : bond 0.00464 ( 36) SS BOND : angle 1.65712 ( 72) hydrogen bonds : bond 0.04556 ( 816) hydrogen bonds : angle 5.98033 ( 2238) link_BETA1-4 : bond 0.01057 ( 21) link_BETA1-4 : angle 4.12467 ( 63) link_NAG-ASN : bond 0.00709 ( 42) link_NAG-ASN : angle 3.48273 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 233 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: C 137 ASN cc_start: 0.7487 (t0) cc_final: 0.6881 (m-40) REVERT: C 170 TYR cc_start: 0.7752 (t80) cc_final: 0.7290 (t80) REVERT: C 298 GLU cc_start: 0.8684 (tp30) cc_final: 0.8461 (tp30) REVERT: C 377 PHE cc_start: 0.6811 (t80) cc_final: 0.6575 (t80) REVERT: C 655 TYR cc_start: 0.8387 (t80) cc_final: 0.7993 (t80) REVERT: C 754 LEU cc_start: 0.8653 (mt) cc_final: 0.8444 (tp) REVERT: A 136 CYS cc_start: 0.6569 (t) cc_final: 0.6112 (p) REVERT: A 140 PHE cc_start: 0.6939 (p90) cc_final: 0.6560 (p90) REVERT: A 141 LEU cc_start: 0.6405 (mm) cc_final: 0.6112 (mt) REVERT: A 176 LEU cc_start: 0.4492 (OUTLIER) cc_final: 0.4128 (pt) REVERT: A 338 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7636 (t80) REVERT: A 377 PHE cc_start: 0.6694 (t80) cc_final: 0.6489 (t80) REVERT: A 655 TYR cc_start: 0.8345 (t80) cc_final: 0.8055 (t80) REVERT: A 1125 ASN cc_start: 0.7460 (t0) cc_final: 0.7154 (t0) REVERT: B 1031 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7913 (mt-10) outliers start: 103 outliers final: 53 residues processed: 318 average time/residue: 0.1607 time to fit residues: 85.9811 Evaluate side-chains 246 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 152 optimal weight: 30.0000 chunk 174 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 277 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN C 245 HIS C 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091818 restraints weight = 51071.010| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.11 r_work: 0.3136 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26913 Z= 0.231 Angle : 0.756 17.715 36786 Z= 0.361 Chirality : 0.051 0.514 4332 Planarity : 0.004 0.060 4650 Dihedral : 12.420 94.290 4819 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.09 % Favored : 90.79 % Rotamer: Outliers : 5.64 % Allowed : 20.92 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.14), residues: 3234 helix: 1.02 (0.21), residues: 615 sheet: -0.53 (0.20), residues: 573 loop : -1.96 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.026 0.002 TYR C 380 PHE 0.028 0.002 PHE C 275 TRP 0.012 0.002 TRP C 633 HIS 0.012 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00536 (26814) covalent geometry : angle 0.70700 (36525) SS BOND : bond 0.00803 ( 36) SS BOND : angle 2.01360 ( 72) hydrogen bonds : bond 0.04539 ( 816) hydrogen bonds : angle 5.75995 ( 2238) link_BETA1-4 : bond 0.01141 ( 21) link_BETA1-4 : angle 4.00684 ( 63) link_NAG-ASN : bond 0.00777 ( 42) link_NAG-ASN : angle 3.39427 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 203 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8347 (tt) REVERT: C 137 ASN cc_start: 0.7861 (t0) cc_final: 0.7072 (m-40) REVERT: C 170 TYR cc_start: 0.8215 (t80) cc_final: 0.7759 (t80) REVERT: C 229 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6273 (pp) REVERT: C 265 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5053 (t80) REVERT: C 266 TYR cc_start: 0.8392 (m-80) cc_final: 0.8068 (m-80) REVERT: C 633 TRP cc_start: 0.7633 (p-90) cc_final: 0.7390 (p-90) REVERT: C 655 TYR cc_start: 0.8633 (t80) cc_final: 0.7897 (t80) REVERT: C 988 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 1050 MET cc_start: 0.8881 (ptt) cc_final: 0.8564 (ptp) REVERT: C 1125 ASN cc_start: 0.7420 (t0) cc_final: 0.6706 (t0) REVERT: A 136 CYS cc_start: 0.6822 (t) cc_final: 0.6278 (p) REVERT: A 141 LEU cc_start: 0.6487 (mm) cc_final: 0.6242 (mt) REVERT: A 176 LEU cc_start: 0.4544 (OUTLIER) cc_final: 0.4101 (pt) REVERT: A 191 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 231 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8784 (pt) REVERT: A 241 LEU cc_start: 0.7326 (mp) cc_final: 0.6809 (mt) REVERT: A 265 TYR cc_start: 0.6186 (OUTLIER) cc_final: 0.5686 (t80) REVERT: A 655 TYR cc_start: 0.8620 (t80) cc_final: 0.8140 (t80) REVERT: A 1125 ASN cc_start: 0.7621 (t0) cc_final: 0.7121 (t0) REVERT: B 229 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6235 (pp) REVERT: B 265 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.5022 (t80) REVERT: B 266 TYR cc_start: 0.8317 (m-80) cc_final: 0.8114 (m-80) REVERT: B 633 TRP cc_start: 0.7820 (p-90) cc_final: 0.7394 (p-90) REVERT: B 754 LEU cc_start: 0.8866 (mt) cc_final: 0.8591 (mt) REVERT: B 1031 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: B 1125 ASN cc_start: 0.7332 (t0) cc_final: 0.6735 (t0) outliers start: 159 outliers final: 94 residues processed: 333 average time/residue: 0.1523 time to fit residues: 86.9677 Evaluate side-chains 266 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 163 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 280 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 318 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 40.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 409 GLN C1005 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.123041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.092721 restraints weight = 50325.293| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.08 r_work: 0.3148 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 26913 Z= 0.166 Angle : 0.698 19.219 36786 Z= 0.332 Chirality : 0.048 0.471 4332 Planarity : 0.004 0.072 4650 Dihedral : 11.266 90.169 4819 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.69 % Favored : 91.28 % Rotamer: Outliers : 4.89 % Allowed : 21.35 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.14), residues: 3234 helix: 1.17 (0.21), residues: 615 sheet: -0.49 (0.19), residues: 603 loop : -2.01 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 457 TYR 0.021 0.002 TYR C 380 PHE 0.023 0.001 PHE B 168 TRP 0.011 0.001 TRP A 633 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00389 (26814) covalent geometry : angle 0.64527 (36525) SS BOND : bond 0.00534 ( 36) SS BOND : angle 2.32598 ( 72) hydrogen bonds : bond 0.03992 ( 816) hydrogen bonds : angle 5.62842 ( 2238) link_BETA1-4 : bond 0.01215 ( 21) link_BETA1-4 : angle 3.95521 ( 63) link_NAG-ASN : bond 0.00646 ( 42) link_NAG-ASN : angle 3.24731 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 180 time to evaluate : 0.919 Fit side-chains REVERT: C 118 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8378 (tt) REVERT: C 170 TYR cc_start: 0.8139 (t80) cc_final: 0.7707 (t80) REVERT: C 229 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6390 (pp) REVERT: C 231 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8893 (pt) REVERT: C 265 TYR cc_start: 0.5834 (OUTLIER) cc_final: 0.4671 (t80) REVERT: C 266 TYR cc_start: 0.8322 (m-80) cc_final: 0.8061 (m-80) REVERT: C 298 GLU cc_start: 0.8726 (tp30) cc_final: 0.8415 (tp30) REVERT: C 655 TYR cc_start: 0.8650 (t80) cc_final: 0.8009 (t80) REVERT: C 988 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8136 (mt-10) REVERT: C 1050 MET cc_start: 0.8896 (ptt) cc_final: 0.8629 (ptp) REVERT: C 1125 ASN cc_start: 0.7476 (t0) cc_final: 0.6689 (t0) REVERT: A 40 ASP cc_start: 0.7740 (m-30) cc_final: 0.7109 (p0) REVERT: A 136 CYS cc_start: 0.6804 (t) cc_final: 0.6271 (p) REVERT: A 176 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.4024 (pt) REVERT: A 265 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5510 (t80) REVERT: A 655 TYR cc_start: 0.8651 (t80) cc_final: 0.8074 (t80) REVERT: A 754 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8329 (mp) REVERT: A 764 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7133 (ttpp) REVERT: A 878 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7782 (mp) REVERT: A 1125 ASN cc_start: 0.7523 (t0) cc_final: 0.6958 (t0) REVERT: B 201 PHE cc_start: 0.5305 (OUTLIER) cc_final: 0.5081 (m-80) REVERT: B 229 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6375 (pp) REVERT: B 266 TYR cc_start: 0.8280 (m-80) cc_final: 0.8047 (m-80) REVERT: B 633 TRP cc_start: 0.7882 (p-90) cc_final: 0.7519 (p-90) REVERT: B 1031 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: B 1125 ASN cc_start: 0.7355 (t0) cc_final: 0.6729 (t0) outliers start: 138 outliers final: 76 residues processed: 298 average time/residue: 0.1328 time to fit residues: 68.2249 Evaluate side-chains 237 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 149 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 102 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 300 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 895 GLN B 409 GLN B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093120 restraints weight = 50303.043| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.08 r_work: 0.3154 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 26913 Z= 0.142 Angle : 0.679 19.064 36786 Z= 0.322 Chirality : 0.048 0.474 4332 Planarity : 0.004 0.075 4650 Dihedral : 10.467 87.278 4819 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.93 % Allowed : 21.67 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.14), residues: 3234 helix: 1.11 (0.21), residues: 633 sheet: -0.55 (0.19), residues: 624 loop : -1.99 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.019 0.001 TYR C 380 PHE 0.035 0.001 PHE B 643 TRP 0.023 0.001 TRP C 633 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00328 (26814) covalent geometry : angle 0.62910 (36525) SS BOND : bond 0.00488 ( 36) SS BOND : angle 1.83813 ( 72) hydrogen bonds : bond 0.03816 ( 816) hydrogen bonds : angle 5.51891 ( 2238) link_BETA1-4 : bond 0.01237 ( 21) link_BETA1-4 : angle 3.86739 ( 63) link_NAG-ASN : bond 0.00640 ( 42) link_NAG-ASN : angle 3.22234 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 177 time to evaluate : 0.945 Fit side-chains REVERT: C 118 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8302 (tt) REVERT: C 170 TYR cc_start: 0.8158 (t80) cc_final: 0.7666 (t80) REVERT: C 229 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6476 (pp) REVERT: C 233 ILE cc_start: 0.8337 (tt) cc_final: 0.8087 (pt) REVERT: C 265 TYR cc_start: 0.5764 (OUTLIER) cc_final: 0.4660 (t80) REVERT: C 298 GLU cc_start: 0.8695 (tp30) cc_final: 0.8381 (tp30) REVERT: C 582 LEU cc_start: 0.8686 (mp) cc_final: 0.8442 (pp) REVERT: C 655 TYR cc_start: 0.8648 (t80) cc_final: 0.8090 (t80) REVERT: C 988 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8194 (mt-10) REVERT: C 1028 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8837 (mttm) REVERT: C 1050 MET cc_start: 0.8896 (ptt) cc_final: 0.8624 (ptp) REVERT: C 1125 ASN cc_start: 0.7521 (t0) cc_final: 0.6664 (t0) REVERT: A 40 ASP cc_start: 0.7830 (m-30) cc_final: 0.7276 (p0) REVERT: A 136 CYS cc_start: 0.6819 (t) cc_final: 0.6299 (p) REVERT: A 176 LEU cc_start: 0.4539 (OUTLIER) cc_final: 0.4068 (pt) REVERT: A 265 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.5380 (t80) REVERT: A 298 GLU cc_start: 0.8625 (tp30) cc_final: 0.8398 (tp30) REVERT: A 655 TYR cc_start: 0.8646 (t80) cc_final: 0.8222 (t80) REVERT: A 754 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 764 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7128 (ttpp) REVERT: A 1028 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8996 (mttm) REVERT: A 1125 ASN cc_start: 0.7444 (t0) cc_final: 0.6859 (t0) REVERT: B 229 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6387 (pp) REVERT: B 265 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.5090 (t80) REVERT: B 388 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8051 (m110) REVERT: B 633 TRP cc_start: 0.7936 (p-90) cc_final: 0.7571 (p-90) REVERT: B 643 PHE cc_start: 0.8255 (t80) cc_final: 0.7598 (t80) REVERT: B 1125 ASN cc_start: 0.7424 (t0) cc_final: 0.6787 (t0) outliers start: 139 outliers final: 90 residues processed: 293 average time/residue: 0.1456 time to fit residues: 72.4623 Evaluate side-chains 260 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 158 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 213 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 317 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 751 ASN B 321 GLN B 493 GLN B 751 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.086013 restraints weight = 51148.037| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.97 r_work: 0.3035 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 26913 Z= 0.389 Angle : 0.855 18.902 36786 Z= 0.416 Chirality : 0.054 0.408 4332 Planarity : 0.005 0.076 4650 Dihedral : 10.072 87.278 4817 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 6.52 % Allowed : 21.28 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.14), residues: 3234 helix: 0.46 (0.20), residues: 633 sheet: -0.66 (0.20), residues: 597 loop : -2.18 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 237 TYR 0.035 0.003 TYR C 380 PHE 0.057 0.002 PHE B 643 TRP 0.021 0.002 TRP A 633 HIS 0.010 0.002 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00929 (26814) covalent geometry : angle 0.80948 (36525) SS BOND : bond 0.00828 ( 36) SS BOND : angle 2.46431 ( 72) hydrogen bonds : bond 0.04864 ( 816) hydrogen bonds : angle 5.85970 ( 2238) link_BETA1-4 : bond 0.01173 ( 21) link_BETA1-4 : angle 3.93889 ( 63) link_NAG-ASN : bond 0.00649 ( 42) link_NAG-ASN : angle 3.50993 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 163 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8557 (tt) REVERT: C 170 TYR cc_start: 0.8387 (t80) cc_final: 0.7856 (t80) REVERT: C 265 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.5911 (t80) REVERT: C 346 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6637 (ttm-80) REVERT: C 365 TYR cc_start: 0.8657 (m-80) cc_final: 0.8403 (m-80) REVERT: C 655 TYR cc_start: 0.8746 (t80) cc_final: 0.8177 (t80) REVERT: C 988 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8303 (mt-10) REVERT: C 1050 MET cc_start: 0.9000 (ptt) cc_final: 0.8703 (ptp) REVERT: C 1125 ASN cc_start: 0.8079 (t0) cc_final: 0.7396 (t0) REVERT: A 176 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4620 (pt) REVERT: A 265 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.5873 (t80) REVERT: A 346 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6668 (ttm-80) REVERT: A 365 TYR cc_start: 0.8760 (m-80) cc_final: 0.8364 (m-80) REVERT: A 655 TYR cc_start: 0.8694 (t80) cc_final: 0.8333 (t80) REVERT: A 754 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 764 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7700 (mtpp) REVERT: A 878 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 996 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8953 (mt) REVERT: A 1014 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8169 (mtt90) REVERT: A 1125 ASN cc_start: 0.7936 (t0) cc_final: 0.7240 (t0) REVERT: B 69 HIS cc_start: 0.5977 (OUTLIER) cc_final: 0.3919 (t70) REVERT: B 229 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6857 (pp) REVERT: B 265 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6501 (t80) REVERT: B 346 ARG cc_start: 0.7120 (mmm160) cc_final: 0.6739 (ttm-80) REVERT: B 633 TRP cc_start: 0.8228 (p-90) cc_final: 0.7837 (p-90) REVERT: B 752 LEU cc_start: 0.9258 (tt) cc_final: 0.9002 (tt) REVERT: B 981 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8754 (mm) REVERT: B 1017 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8012 (tt0) REVERT: B 1107 ARG cc_start: 0.8283 (mpt-90) cc_final: 0.7983 (mpt-90) REVERT: B 1125 ASN cc_start: 0.7875 (t0) cc_final: 0.7542 (t0) outliers start: 184 outliers final: 115 residues processed: 322 average time/residue: 0.1676 time to fit residues: 89.4553 Evaluate side-chains 265 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 137 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 190 optimal weight: 0.7980 chunk 260 optimal weight: 50.0000 chunk 261 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 301 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 274 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 317 ASN A 690 GLN B 317 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090581 restraints weight = 50163.671| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.96 r_work: 0.3115 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 26913 Z= 0.156 Angle : 0.707 18.817 36786 Z= 0.341 Chirality : 0.049 0.431 4332 Planarity : 0.004 0.084 4650 Dihedral : 9.494 85.720 4817 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 4.50 % Allowed : 22.80 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.14), residues: 3234 helix: 0.90 (0.21), residues: 633 sheet: -0.63 (0.21), residues: 576 loop : -2.04 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.021 0.002 TYR C 380 PHE 0.028 0.001 PHE B 643 TRP 0.025 0.001 TRP A 633 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00371 (26814) covalent geometry : angle 0.65818 (36525) SS BOND : bond 0.00755 ( 36) SS BOND : angle 1.95890 ( 72) hydrogen bonds : bond 0.03967 ( 816) hydrogen bonds : angle 5.69450 ( 2238) link_BETA1-4 : bond 0.01241 ( 21) link_BETA1-4 : angle 3.84312 ( 63) link_NAG-ASN : bond 0.00628 ( 42) link_NAG-ASN : angle 3.26595 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 165 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 118 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8470 (tt) REVERT: C 170 TYR cc_start: 0.8315 (t80) cc_final: 0.7758 (t80) REVERT: C 265 TYR cc_start: 0.6182 (OUTLIER) cc_final: 0.5005 (t80) REVERT: C 266 TYR cc_start: 0.8553 (m-80) cc_final: 0.8117 (m-80) REVERT: C 298 GLU cc_start: 0.8664 (tp30) cc_final: 0.8314 (tp30) REVERT: C 365 TYR cc_start: 0.8613 (m-80) cc_final: 0.8261 (m-80) REVERT: C 655 TYR cc_start: 0.8679 (t80) cc_final: 0.8210 (t80) REVERT: C 988 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8252 (mt-10) REVERT: C 1028 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8951 (mttm) REVERT: C 1050 MET cc_start: 0.8939 (ptt) cc_final: 0.8647 (ptp) REVERT: C 1125 ASN cc_start: 0.7875 (t0) cc_final: 0.7058 (t0) REVERT: A 176 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4527 (pt) REVERT: A 265 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5417 (t80) REVERT: A 346 ARG cc_start: 0.6763 (mmm160) cc_final: 0.6425 (ttm-80) REVERT: A 365 TYR cc_start: 0.8587 (m-80) cc_final: 0.8114 (m-80) REVERT: A 655 TYR cc_start: 0.8651 (t80) cc_final: 0.8368 (t80) REVERT: A 754 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 878 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 1125 ASN cc_start: 0.7822 (t0) cc_final: 0.7134 (t0) REVERT: B 265 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.5974 (t80) REVERT: B 294 ASP cc_start: 0.7632 (m-30) cc_final: 0.7417 (m-30) REVERT: B 633 TRP cc_start: 0.8061 (p-90) cc_final: 0.7714 (p-90) REVERT: B 752 LEU cc_start: 0.9193 (tt) cc_final: 0.8942 (tt) REVERT: B 981 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8722 (mm) REVERT: B 1107 ARG cc_start: 0.8234 (mpt-90) cc_final: 0.8025 (mpt-90) REVERT: B 1125 ASN cc_start: 0.7781 (t0) cc_final: 0.7361 (t0) outliers start: 127 outliers final: 91 residues processed: 272 average time/residue: 0.1485 time to fit residues: 67.8515 Evaluate side-chains 245 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 144 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 47 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 274 optimal weight: 9.9990 chunk 311 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 301 optimal weight: 0.7980 chunk 48 optimal weight: 0.0170 chunk 146 optimal weight: 5.9990 chunk 294 optimal weight: 0.0870 chunk 139 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS A 690 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.120237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090773 restraints weight = 49951.818| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.04 r_work: 0.3117 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26913 Z= 0.132 Angle : 0.687 18.933 36786 Z= 0.327 Chirality : 0.047 0.408 4332 Planarity : 0.004 0.082 4650 Dihedral : 8.692 82.718 4817 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.08 % Allowed : 23.69 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.14), residues: 3234 helix: 1.08 (0.21), residues: 627 sheet: -0.51 (0.21), residues: 573 loop : -1.99 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.017 0.001 TYR C 265 PHE 0.021 0.001 PHE B 643 TRP 0.022 0.001 TRP A 633 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00304 (26814) covalent geometry : angle 0.63940 (36525) SS BOND : bond 0.00494 ( 36) SS BOND : angle 1.88210 ( 72) hydrogen bonds : bond 0.03750 ( 816) hydrogen bonds : angle 5.51895 ( 2238) link_BETA1-4 : bond 0.01233 ( 21) link_BETA1-4 : angle 3.73005 ( 63) link_NAG-ASN : bond 0.00632 ( 42) link_NAG-ASN : angle 3.23850 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 177 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8417 (tt) REVERT: C 170 TYR cc_start: 0.8204 (t80) cc_final: 0.7656 (t80) REVERT: C 196 ASN cc_start: 0.7526 (p0) cc_final: 0.6897 (t0) REVERT: C 265 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.4902 (t80) REVERT: C 266 TYR cc_start: 0.8247 (m-80) cc_final: 0.7940 (m-80) REVERT: C 298 GLU cc_start: 0.8695 (tp30) cc_final: 0.8355 (tp30) REVERT: C 365 TYR cc_start: 0.8608 (m-80) cc_final: 0.8251 (m-80) REVERT: C 655 TYR cc_start: 0.8639 (t80) cc_final: 0.8208 (t80) REVERT: C 895 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: C 988 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8169 (mt-10) REVERT: C 1050 MET cc_start: 0.8972 (ptt) cc_final: 0.8693 (ptp) REVERT: C 1125 ASN cc_start: 0.7848 (t0) cc_final: 0.7010 (t0) REVERT: A 176 LEU cc_start: 0.4940 (OUTLIER) cc_final: 0.4425 (pt) REVERT: A 265 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5469 (t80) REVERT: A 346 ARG cc_start: 0.6808 (mmm160) cc_final: 0.6437 (ttm-80) REVERT: A 365 TYR cc_start: 0.8640 (m-80) cc_final: 0.8218 (m-80) REVERT: A 655 TYR cc_start: 0.8663 (t80) cc_final: 0.8364 (t80) REVERT: A 754 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8588 (tt) REVERT: A 1125 ASN cc_start: 0.7726 (t0) cc_final: 0.7051 (t0) REVERT: B 265 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.5867 (t80) REVERT: B 266 TYR cc_start: 0.8352 (m-80) cc_final: 0.8070 (m-80) REVERT: B 495 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.5792 (t80) REVERT: B 633 TRP cc_start: 0.8063 (p-90) cc_final: 0.7726 (p-90) REVERT: B 752 LEU cc_start: 0.9199 (tt) cc_final: 0.8940 (tp) REVERT: B 981 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8675 (mm) REVERT: B 1125 ASN cc_start: 0.7678 (t0) cc_final: 0.7218 (t0) outliers start: 115 outliers final: 86 residues processed: 272 average time/residue: 0.1460 time to fit residues: 68.7110 Evaluate side-chains 244 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 149 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.8433 > 50: distance: 18 - 25: 11.157 distance: 25 - 26: 6.121 distance: 26 - 27: 8.441 distance: 26 - 29: 8.273 distance: 27 - 28: 26.610 distance: 29 - 30: 3.150 distance: 30 - 31: 5.961 distance: 30 - 32: 3.175 distance: 31 - 33: 6.176 distance: 32 - 34: 6.700 distance: 34 - 35: 3.059 distance: 36 - 37: 16.020 distance: 37 - 38: 8.890 distance: 37 - 40: 24.219 distance: 38 - 39: 33.805 distance: 38 - 41: 14.115 distance: 41 - 42: 8.620 distance: 42 - 43: 4.213 distance: 42 - 45: 7.404 distance: 43 - 44: 5.217 distance: 43 - 52: 5.517 distance: 45 - 46: 6.253 distance: 46 - 47: 17.975 distance: 46 - 48: 16.409 distance: 47 - 49: 30.159 distance: 48 - 50: 18.501 distance: 49 - 51: 10.895 distance: 50 - 51: 14.472 distance: 52 - 53: 15.033 distance: 53 - 54: 12.922 distance: 53 - 56: 20.806 distance: 54 - 55: 24.772 distance: 54 - 61: 22.416 distance: 56 - 57: 16.850 distance: 58 - 59: 5.785 distance: 59 - 60: 47.933 distance: 61 - 62: 30.395 distance: 62 - 63: 13.426 distance: 63 - 64: 15.598 distance: 63 - 67: 10.231 distance: 65 - 66: 29.924 distance: 66 - 148: 29.077 distance: 68 - 69: 15.930 distance: 68 - 71: 12.430 distance: 69 - 70: 29.056 distance: 69 - 79: 16.725 distance: 72 - 73: 6.971 distance: 72 - 74: 6.860 distance: 73 - 75: 7.410 distance: 75 - 77: 13.333 distance: 76 - 77: 12.645 distance: 77 - 78: 6.718 distance: 80 - 81: 12.395 distance: 81 - 82: 38.289 distance: 81 - 83: 8.212 distance: 83 - 84: 7.314 distance: 84 - 85: 38.226 distance: 84 - 87: 10.820 distance: 85 - 90: 25.250 distance: 87 - 88: 7.587 distance: 87 - 89: 30.571 distance: 90 - 91: 37.524 distance: 91 - 92: 25.585 distance: 92 - 93: 6.312 distance: 92 - 96: 35.935 distance: 96 - 97: 22.754 distance: 96 - 102: 27.515 distance: 97 - 98: 5.955 distance: 97 - 100: 10.143 distance: 98 - 99: 13.565 distance: 98 - 103: 25.055 distance: 100 - 101: 18.182 distance: 101 - 102: 17.215