Starting phenix.real_space_refine on Mon Aug 25 08:01:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5r_38073/08_2025/8x5r_38073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5r_38073/08_2025/8x5r_38073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5r_38073/08_2025/8x5r_38073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5r_38073/08_2025/8x5r_38073.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5r_38073/08_2025/8x5r_38073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5r_38073/08_2025/8x5r_38073.cif" } resolution = 3.72 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= 0.052 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 91 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: 6.70, per 1000 atoms: 0.26 Number of scatterers: 26208 At special positions: 0 Unit cell: (151, 141, 192, 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 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 657 " " NAG C1305 " - " ASN C 331 " " 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 C1098 " " NAG H 1 " - " ASN C1134 " " NAG I 1 " - " ASN C 343 " " NAG J 1 " - " ASN C 354 " " 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 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: 54 helices and 50 sheets defined 21.7% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'C' and resid 69 through 73 removed outlier: 4.010A pdb=" N THR C 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.030A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.457A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.796A 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: 3.683A 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 removed outlier: 3.580A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 941 removed outlier: 4.575A pdb=" N VAL C 915 " --> pdb=" O VAL C 911 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.582A 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: 4.297A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 removed outlier: 3.999A pdb=" N SER A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 367 through 371 removed outlier: 4.051A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 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: 3.826A 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 869 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 911 through 941 removed outlier: 4.479A pdb=" N VAL A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.604A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.434A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 4.505A pdb=" N THR B 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.777A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.818A 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 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 911 through 941 removed outlier: 4.513A pdb=" N VAL B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.502A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.653A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.468A 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: 7.641A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.858A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 55 removed outlier: 7.492A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 172 removed outlier: 6.539A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.125A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.308A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.687A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 656 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.772A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'C' and resid 719 through 722 removed outlier: 3.504A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 719 through 722 removed outlier: 7.190A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 790 removed outlier: 5.678A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.968A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.501A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.659A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.524A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.044A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.466A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.943A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.432A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 removed outlier: 4.294A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.468A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.681A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.508A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'A' and resid 719 through 727 removed outlier: 3.565A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AD8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.454A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.931A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.575A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.219A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AE5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.587A pdb=" N ALA B 397 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.244A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.319A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.489A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.694A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'B' and resid 719 through 727 removed outlier: 7.372A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AF5, first strand: chain 'B' and resid 1094 through 1097 809 hydrogen bonds defined for protein. 2202 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: 6.31 Time building geometry restraints manager: 3.29 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: 8240 1.34 - 1.46: 6414 1.46 - 1.59: 12022 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 26814 Sorted by residual: bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" N ILE C 714 " pdb=" CA ILE C 714 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.70e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.58e+01 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 34874 1.95 - 3.91: 1473 3.91 - 5.86: 132 5.86 - 7.82: 34 7.82 - 9.77: 12 Bond angle restraints: 36525 Sorted by residual: angle pdb=" N THR B 604 " pdb=" CA THR B 604 " pdb=" C THR B 604 " ideal model delta sigma weight residual 114.62 107.40 7.22 1.14e+00 7.69e-01 4.01e+01 angle pdb=" N VAL C 159 " pdb=" CA VAL C 159 " pdb=" C VAL C 159 " ideal model delta sigma weight residual 113.20 107.29 5.91 9.60e-01 1.09e+00 3.79e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 114.62 107.96 6.66 1.14e+00 7.69e-01 3.42e+01 angle pdb=" N PHE C 855 " pdb=" CA PHE C 855 " pdb=" C PHE C 855 " ideal model delta sigma weight residual 112.25 104.47 7.78 1.36e+00 5.41e-01 3.27e+01 angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 122.65 113.81 8.84 1.66e+00 3.63e-01 2.83e+01 ... (remaining 36520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 14936 23.25 - 46.50: 1383 46.50 - 69.75: 251 69.75 - 92.99: 98 92.99 - 116.24: 105 Dihedral angle restraints: 16773 sinusoidal: 7287 harmonic: 9486 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 171.21 -78.21 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -14.10 -71.90 1 1.00e+01 1.00e-02 6.62e+01 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 35.05 57.95 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 16770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4072 0.106 - 0.212: 243 0.212 - 0.318: 7 0.318 - 0.423: 7 0.423 - 0.529: 3 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.60e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.25e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.12e+01 ... (remaining 4329 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " 0.327 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG B1307 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " -0.508 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " -0.321 2.00e-02 2.50e+03 2.78e-01 9.63e+02 pdb=" C7 NAG C1306 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.134 2.00e-02 2.50e+03 1.14e-01 1.61e+02 pdb=" C7 NAG R 1 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.185 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.105 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2476 2.74 - 3.28: 27807 3.28 - 3.82: 44560 3.82 - 4.36: 51294 4.36 - 4.90: 87493 Nonbonded interactions: 213630 Sorted by model distance: nonbonded pdb=" O GLN B 580 " pdb=" O3 NAG B1305 " model vdw 2.203 3.040 nonbonded pdb=" O VAL B 608 " pdb=" OH TYR B 636 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.208 3.040 nonbonded pdb=" NZ LYS A 386 " pdb=" O LEU B 984 " model vdw 2.213 3.120 nonbonded pdb=" O ILE B 805 " pdb=" OG SER B 816 " model vdw 2.225 3.040 ... (remaining 213625 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.200 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.120 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 0.094 26913 Z= 0.348 Angle : 0.876 10.563 36786 Z= 0.503 Chirality : 0.056 0.529 4332 Planarity : 0.009 0.285 4650 Dihedral : 20.776 116.242 10569 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.21 % Favored : 90.26 % Rotamer: Outliers : 1.06 % Allowed : 23.58 % Favored : 75.35 % 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: -1.84 (0.14), residues: 3234 helix: 0.71 (0.21), residues: 641 sheet: -0.68 (0.20), residues: 622 loop : -2.20 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.024 0.002 TYR C 423 PHE 0.042 0.002 PHE A 201 TRP 0.015 0.002 TRP B 633 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00576 (26814) covalent geometry : angle 0.84540 (36525) SS BOND : bond 0.00416 ( 36) SS BOND : angle 1.92766 ( 72) hydrogen bonds : bond 0.20461 ( 805) hydrogen bonds : angle 8.37076 ( 2202) link_BETA1-4 : bond 0.01258 ( 21) link_BETA1-4 : angle 4.19122 ( 63) link_NAG-ASN : bond 0.00539 ( 42) link_NAG-ASN : angle 2.42066 ( 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 166 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 PRO cc_start: 0.8037 (OUTLIER) cc_final: 0.7055 (Cg_endo) REVERT: C 140 PHE cc_start: 0.7020 (t80) cc_final: 0.6706 (t80) REVERT: C 902 MET cc_start: 0.8824 (tpp) cc_final: 0.8617 (tpt) REVERT: A 835 LYS cc_start: 0.3154 (OUTLIER) cc_final: 0.2330 (pttm) REVERT: A 1030 SER cc_start: 0.8973 (m) cc_final: 0.8180 (m) REVERT: B 1079 PRO cc_start: 0.9141 (Cg_exo) cc_final: 0.8828 (Cg_endo) outliers start: 30 outliers final: 6 residues processed: 160 average time/residue: 0.1755 time to fit residues: 46.6078 Evaluate side-chains 116 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 456 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN C1088 HIS A 81 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 164 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 644 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1011 GLN B1054 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.106728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072314 restraints weight = 84772.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.074639 restraints weight = 44262.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.076130 restraints weight = 29336.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.076976 restraints weight = 22732.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.077591 restraints weight = 19589.300| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26913 Z= 0.215 Angle : 0.770 12.093 36786 Z= 0.370 Chirality : 0.050 0.344 4332 Planarity : 0.005 0.057 4650 Dihedral : 16.463 101.626 4827 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.81 % Favored : 90.85 % Rotamer: Outliers : 3.09 % Allowed : 22.16 % Favored : 74.75 % 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: -1.74 (0.14), residues: 3234 helix: 0.89 (0.21), residues: 639 sheet: -0.58 (0.21), residues: 573 loop : -2.14 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 815 TYR 0.022 0.002 TYR B1067 PHE 0.019 0.002 PHE B 643 TRP 0.015 0.002 TRP A 64 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00490 (26814) covalent geometry : angle 0.74227 (36525) SS BOND : bond 0.00504 ( 36) SS BOND : angle 1.73887 ( 72) hydrogen bonds : bond 0.04800 ( 805) hydrogen bonds : angle 6.44936 ( 2202) link_BETA1-4 : bond 0.01116 ( 21) link_BETA1-4 : angle 3.69466 ( 63) link_NAG-ASN : bond 0.00561 ( 42) link_NAG-ASN : angle 2.19750 ( 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 210 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 123 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 974 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8798 (t) REVERT: C 1041 ASP cc_start: 0.8124 (t0) cc_final: 0.7319 (t0) REVERT: A 54 LEU cc_start: 0.8315 (mm) cc_final: 0.7632 (tp) REVERT: A 423 TYR cc_start: 0.5238 (t80) cc_final: 0.4885 (t80) REVERT: A 434 ILE cc_start: -0.0296 (OUTLIER) cc_final: -0.0548 (mt) REVERT: A 709 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7934 (p0) REVERT: A 724 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9011 (p) REVERT: A 835 LYS cc_start: 0.3081 (OUTLIER) cc_final: 0.2225 (pttm) REVERT: A 1030 SER cc_start: 0.9195 (m) cc_final: 0.8694 (m) REVERT: A 1107 ARG cc_start: 0.7735 (mmp-170) cc_final: 0.7320 (tpt90) REVERT: B 409 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: B 468 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8411 (tt) outliers start: 87 outliers final: 42 residues processed: 201 average time/residue: 0.1579 time to fit residues: 54.0726 Evaluate side-chains 152 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 249 optimal weight: 5.9990 chunk 302 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 265 optimal weight: 0.7980 chunk 33 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 644 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 901 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 625 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.108503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074683 restraints weight = 84703.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.077130 restraints weight = 42977.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078688 restraints weight = 27919.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.079698 restraints weight = 21285.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.080281 restraints weight = 18052.808| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26913 Z= 0.133 Angle : 0.705 11.831 36786 Z= 0.333 Chirality : 0.048 0.311 4332 Planarity : 0.004 0.051 4650 Dihedral : 13.514 95.941 4819 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.82 % Favored : 91.90 % Rotamer: Outliers : 2.84 % Allowed : 22.38 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.61 (0.14), residues: 3234 helix: 1.11 (0.21), residues: 643 sheet: -0.53 (0.20), residues: 618 loop : -2.13 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 403 TYR 0.016 0.001 TYR A1067 PHE 0.023 0.001 PHE A 106 TRP 0.018 0.001 TRP C 633 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00289 (26814) covalent geometry : angle 0.67655 (36525) SS BOND : bond 0.00389 ( 36) SS BOND : angle 1.56253 ( 72) hydrogen bonds : bond 0.04083 ( 805) hydrogen bonds : angle 5.93073 ( 2202) link_BETA1-4 : bond 0.01171 ( 21) link_BETA1-4 : angle 3.65876 ( 63) link_NAG-ASN : bond 0.00410 ( 42) link_NAG-ASN : angle 2.09016 ( 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 213 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 133 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.6944 (p) REVERT: C 617 CYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5691 (m) REVERT: C 633 TRP cc_start: 0.4774 (p-90) cc_final: 0.4281 (p-90) REVERT: C 1041 ASP cc_start: 0.8060 (t0) cc_final: 0.7253 (t0) REVERT: A 54 LEU cc_start: 0.8240 (mm) cc_final: 0.7532 (tp) REVERT: A 423 TYR cc_start: 0.5157 (t80) cc_final: 0.4899 (t80) REVERT: A 724 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8819 (p) REVERT: A 835 LYS cc_start: 0.2982 (OUTLIER) cc_final: 0.2187 (pttm) REVERT: A 904 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.7413 (m-10) REVERT: A 1030 SER cc_start: 0.9160 (m) cc_final: 0.8509 (m) REVERT: A 1107 ARG cc_start: 0.7740 (mmp-170) cc_final: 0.7201 (tpt90) REVERT: B 200 TYR cc_start: 0.7721 (m-80) cc_final: 0.7391 (m-80) REVERT: B 230 PRO cc_start: 0.8015 (Cg_exo) cc_final: 0.7794 (Cg_endo) REVERT: B 1041 ASP cc_start: 0.8361 (t70) cc_final: 0.8094 (t70) outliers start: 80 outliers final: 30 residues processed: 204 average time/residue: 0.1648 time to fit residues: 56.6011 Evaluate side-chains 146 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 318 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 30.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 751 ASN ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 762 GLN B 125 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.106151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072021 restraints weight = 84159.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074348 restraints weight = 43496.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.075839 restraints weight = 28648.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.076804 restraints weight = 22019.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077376 restraints weight = 18766.790| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26913 Z= 0.189 Angle : 0.731 12.495 36786 Z= 0.346 Chirality : 0.048 0.272 4332 Planarity : 0.004 0.051 4650 Dihedral : 11.645 90.025 4817 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.29 % Favored : 91.47 % Rotamer: Outliers : 3.55 % Allowed : 22.20 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.60 (0.14), residues: 3234 helix: 1.10 (0.21), residues: 641 sheet: -0.69 (0.21), residues: 560 loop : -2.02 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 567 TYR 0.016 0.001 TYR B1067 PHE 0.024 0.001 PHE A 106 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00436 (26814) covalent geometry : angle 0.69791 (36525) SS BOND : bond 0.00434 ( 36) SS BOND : angle 1.87869 ( 72) hydrogen bonds : bond 0.04104 ( 805) hydrogen bonds : angle 5.84376 ( 2202) link_BETA1-4 : bond 0.01105 ( 21) link_BETA1-4 : angle 3.73005 ( 63) link_NAG-ASN : bond 0.00339 ( 42) link_NAG-ASN : angle 2.43797 ( 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 222 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 122 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8205 (mm) cc_final: 0.7148 (tp) REVERT: A 423 TYR cc_start: 0.5372 (t80) cc_final: 0.5146 (t80) REVERT: A 571 ASP cc_start: 0.5018 (m-30) cc_final: 0.4815 (m-30) REVERT: A 724 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 835 LYS cc_start: 0.3082 (OUTLIER) cc_final: 0.2246 (pttm) REVERT: A 1092 GLU cc_start: 0.7815 (pp20) cc_final: 0.7559 (pp20) REVERT: A 1107 ARG cc_start: 0.7823 (mmp-170) cc_final: 0.7534 (mmm160) REVERT: B 388 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7609 (m-40) REVERT: B 674 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8437 (t80) REVERT: B 756 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8470 (t80) REVERT: B 1041 ASP cc_start: 0.8409 (t70) cc_final: 0.8115 (t70) outliers start: 100 outliers final: 59 residues processed: 211 average time/residue: 0.1593 time to fit residues: 57.5524 Evaluate side-chains 166 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 102 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 102 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 300 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.104475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.070448 restraints weight = 84335.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072644 restraints weight = 45220.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073971 restraints weight = 30370.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074944 restraints weight = 23798.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075443 restraints weight = 20408.432| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26913 Z= 0.233 Angle : 0.748 15.602 36786 Z= 0.357 Chirality : 0.048 0.286 4332 Planarity : 0.004 0.052 4650 Dihedral : 10.735 89.421 4817 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.60 % Favored : 91.19 % Rotamer: Outliers : 3.62 % Allowed : 22.94 % 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: -1.66 (0.14), residues: 3234 helix: 0.85 (0.21), residues: 655 sheet: -0.74 (0.21), residues: 547 loop : -2.00 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.020 0.002 TYR C 265 PHE 0.019 0.001 PHE A 106 TRP 0.018 0.002 TRP C 633 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00540 (26814) covalent geometry : angle 0.70962 (36525) SS BOND : bond 0.00446 ( 36) SS BOND : angle 2.79777 ( 72) hydrogen bonds : bond 0.04193 ( 805) hydrogen bonds : angle 5.85436 ( 2202) link_BETA1-4 : bond 0.01065 ( 21) link_BETA1-4 : angle 3.80382 ( 63) link_NAG-ASN : bond 0.00314 ( 42) link_NAG-ASN : angle 2.36522 ( 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 213 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 111 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: -0.3484 (OUTLIER) cc_final: -0.3711 (t) REVERT: A 166 CYS cc_start: -0.0365 (OUTLIER) cc_final: -0.1512 (t) REVERT: A 423 TYR cc_start: 0.5458 (t80) cc_final: 0.5142 (t80) REVERT: A 464 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: A 835 LYS cc_start: 0.3273 (OUTLIER) cc_final: 0.2384 (pttm) REVERT: A 1092 GLU cc_start: 0.7753 (pp20) cc_final: 0.7418 (pp20) REVERT: A 1107 ARG cc_start: 0.7824 (mmp-170) cc_final: 0.7533 (mmm160) REVERT: B 388 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7654 (m110) REVERT: B 674 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8491 (t80) REVERT: B 755 GLN cc_start: 0.8933 (pp30) cc_final: 0.8731 (pp30) REVERT: B 763 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8682 (tt) outliers start: 102 outliers final: 68 residues processed: 203 average time/residue: 0.1653 time to fit residues: 56.4664 Evaluate side-chains 179 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 104 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 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 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS 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: 2.9990 chunk 305 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN C 836 GLN A 52 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.102924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.069699 restraints weight = 84110.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.072368 restraints weight = 47997.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072727 restraints weight = 27946.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073125 restraints weight = 24918.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.073223 restraints weight = 23189.415| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 26913 Z= 0.268 Angle : 0.761 11.935 36786 Z= 0.367 Chirality : 0.049 0.294 4332 Planarity : 0.005 0.086 4650 Dihedral : 10.062 83.110 4816 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.18 % Favored : 90.60 % Rotamer: Outliers : 4.15 % Allowed : 23.12 % Favored : 72.73 % 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: -1.76 (0.14), residues: 3234 helix: 0.68 (0.21), residues: 664 sheet: -0.80 (0.21), residues: 547 loop : -2.04 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 567 TYR 0.022 0.002 TYR B 636 PHE 0.016 0.002 PHE C 392 TRP 0.020 0.002 TRP C 633 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00620 (26814) covalent geometry : angle 0.72920 (36525) SS BOND : bond 0.00565 ( 36) SS BOND : angle 2.20151 ( 72) hydrogen bonds : bond 0.04313 ( 805) hydrogen bonds : angle 5.91523 ( 2202) link_BETA1-4 : bond 0.01087 ( 21) link_BETA1-4 : angle 3.87103 ( 63) link_NAG-ASN : bond 0.00344 ( 42) link_NAG-ASN : angle 2.18890 ( 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 232 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 115 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7256 (t0) REVERT: C 241 LEU cc_start: 0.7614 (mp) cc_final: 0.7254 (mp) REVERT: C 974 SER cc_start: 0.9409 (OUTLIER) cc_final: 0.8998 (t) REVERT: A 131 CYS cc_start: -0.3431 (OUTLIER) cc_final: -0.4098 (t) REVERT: A 166 CYS cc_start: -0.0289 (OUTLIER) cc_final: -0.1389 (t) REVERT: A 423 TYR cc_start: 0.5678 (t80) cc_final: 0.5399 (t80) REVERT: A 464 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: A 835 LYS cc_start: 0.3595 (OUTLIER) cc_final: 0.2620 (pttm) REVERT: A 1107 ARG cc_start: 0.7861 (mmp-170) cc_final: 0.7508 (mmm160) REVERT: B 388 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7744 (m110) REVERT: B 564 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.5915 (tp40) REVERT: B 755 GLN cc_start: 0.8971 (pp30) cc_final: 0.8682 (pp30) REVERT: B 763 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8710 (tt) outliers start: 117 outliers final: 83 residues processed: 221 average time/residue: 0.1617 time to fit residues: 60.3725 Evaluate side-chains 199 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 107 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 190 optimal weight: 0.8980 chunk 260 optimal weight: 10.0000 chunk 261 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 274 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN A 52 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 762 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.105191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072258 restraints weight = 83393.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074840 restraints weight = 46602.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075558 restraints weight = 26796.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.075975 restraints weight = 22141.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.076060 restraints weight = 21006.332| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26913 Z= 0.134 Angle : 0.686 13.809 36786 Z= 0.325 Chirality : 0.047 0.284 4332 Planarity : 0.004 0.054 4650 Dihedral : 9.335 79.551 4816 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.13 % Favored : 91.77 % Rotamer: Outliers : 3.23 % Allowed : 24.04 % Favored : 72.73 % 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: -1.61 (0.14), residues: 3234 helix: 0.89 (0.21), residues: 661 sheet: -0.68 (0.21), residues: 536 loop : -1.97 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 454 TYR 0.020 0.001 TYR C 707 PHE 0.033 0.001 PHE A 106 TRP 0.024 0.002 TRP C 633 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00306 (26814) covalent geometry : angle 0.65537 (36525) SS BOND : bond 0.00451 ( 36) SS BOND : angle 1.72640 ( 72) hydrogen bonds : bond 0.03853 ( 805) hydrogen bonds : angle 5.68065 ( 2202) link_BETA1-4 : bond 0.01090 ( 21) link_BETA1-4 : angle 3.85525 ( 63) link_NAG-ASN : bond 0.00283 ( 42) link_NAG-ASN : angle 1.95182 ( 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 211 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 120 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 CYS cc_start: -0.0513 (OUTLIER) cc_final: -0.1473 (t) REVERT: A 211 ASN cc_start: 0.4232 (OUTLIER) cc_final: 0.2849 (t0) REVERT: A 456 PHE cc_start: 0.8377 (m-10) cc_final: 0.8167 (m-80) REVERT: A 464 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: A 835 LYS cc_start: 0.3453 (OUTLIER) cc_final: 0.2482 (pttm) REVERT: A 1107 ARG cc_start: 0.7867 (mmp-170) cc_final: 0.7482 (mmm160) REVERT: B 388 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7646 (m110) REVERT: B 755 GLN cc_start: 0.8884 (pp30) cc_final: 0.8606 (pp30) REVERT: B 763 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8657 (tt) REVERT: B 985 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7845 (m-30) outliers start: 91 outliers final: 61 residues processed: 205 average time/residue: 0.1622 time to fit residues: 56.8735 Evaluate side-chains 174 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 106 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 47 optimal weight: 40.0000 chunk 164 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 311 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 301 optimal weight: 0.0670 chunk 48 optimal weight: 20.0000 chunk 146 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 139 optimal weight: 0.0030 overall best weight: 1.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 853 GLN C 895 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1054 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.104712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.071945 restraints weight = 83901.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.073625 restraints weight = 51252.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.074485 restraints weight = 30657.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074824 restraints weight = 28362.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074844 restraints weight = 24321.712| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26913 Z= 0.151 Angle : 0.684 13.892 36786 Z= 0.325 Chirality : 0.047 0.283 4332 Planarity : 0.004 0.054 4650 Dihedral : 8.830 77.536 4816 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.50 % Favored : 91.40 % Rotamer: Outliers : 3.01 % Allowed : 24.57 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.61 (0.14), residues: 3234 helix: 1.03 (0.21), residues: 645 sheet: -0.69 (0.21), residues: 568 loop : -2.00 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 498 TYR 0.016 0.001 TYR C 707 PHE 0.029 0.001 PHE C 168 TRP 0.024 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00347 (26814) covalent geometry : angle 0.65330 (36525) SS BOND : bond 0.00374 ( 36) SS BOND : angle 1.95513 ( 72) hydrogen bonds : bond 0.03779 ( 805) hydrogen bonds : angle 5.64853 ( 2202) link_BETA1-4 : bond 0.01089 ( 21) link_BETA1-4 : angle 3.81098 ( 63) link_NAG-ASN : bond 0.00291 ( 42) link_NAG-ASN : angle 1.90341 ( 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 197 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 112 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 900 MET cc_start: 0.8520 (mmm) cc_final: 0.7890 (mmt) REVERT: C 1141 LEU cc_start: 0.9149 (mt) cc_final: 0.8863 (pp) REVERT: A 211 ASN cc_start: 0.4260 (OUTLIER) cc_final: 0.2843 (t0) REVERT: A 456 PHE cc_start: 0.8402 (m-10) cc_final: 0.8180 (m-80) REVERT: A 464 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: A 835 LYS cc_start: 0.3560 (OUTLIER) cc_final: 0.2409 (pttm) REVERT: A 1107 ARG cc_start: 0.7869 (mmp-170) cc_final: 0.7499 (mmm160) REVERT: B 388 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7669 (m110) REVERT: B 755 GLN cc_start: 0.8920 (pp30) cc_final: 0.8627 (pp30) REVERT: B 763 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8655 (tt) REVERT: B 985 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7857 (m-30) outliers start: 85 outliers final: 67 residues processed: 191 average time/residue: 0.1595 time to fit residues: 51.8973 Evaluate side-chains 183 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 110 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 255 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 136 optimal weight: 0.0670 chunk 250 optimal weight: 0.5980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.105192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072623 restraints weight = 83926.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.073949 restraints weight = 53120.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.074428 restraints weight = 33342.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074759 restraints weight = 33804.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074890 restraints weight = 28291.848| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26913 Z= 0.133 Angle : 0.674 15.392 36786 Z= 0.320 Chirality : 0.046 0.280 4332 Planarity : 0.004 0.054 4650 Dihedral : 8.436 75.484 4816 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.10 % Favored : 91.81 % Rotamer: Outliers : 2.84 % Allowed : 24.72 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.57 (0.14), residues: 3234 helix: 0.95 (0.21), residues: 654 sheet: -0.58 (0.20), residues: 610 loop : -2.01 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 454 TYR 0.016 0.001 TYR C 707 PHE 0.024 0.001 PHE C 168 TRP 0.025 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00306 (26814) covalent geometry : angle 0.64317 (36525) SS BOND : bond 0.00409 ( 36) SS BOND : angle 1.93297 ( 72) hydrogen bonds : bond 0.03727 ( 805) hydrogen bonds : angle 5.58235 ( 2202) link_BETA1-4 : bond 0.01088 ( 21) link_BETA1-4 : angle 3.77578 ( 63) link_NAG-ASN : bond 0.00261 ( 42) link_NAG-ASN : angle 1.83501 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 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 197 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 117 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 498 ARG cc_start: 0.8139 (mmt-90) cc_final: 0.7602 (mmp80) REVERT: C 900 MET cc_start: 0.8494 (mmm) cc_final: 0.7859 (mmt) REVERT: C 1141 LEU cc_start: 0.9160 (mt) cc_final: 0.8878 (pp) REVERT: A 211 ASN cc_start: 0.4239 (OUTLIER) cc_final: 0.2814 (t0) REVERT: A 456 PHE cc_start: 0.8428 (m-10) cc_final: 0.8199 (m-80) REVERT: A 464 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: A 835 LYS cc_start: 0.3592 (OUTLIER) cc_final: 0.2434 (pttm) REVERT: A 1107 ARG cc_start: 0.7914 (mmp-170) cc_final: 0.7531 (mmm160) REVERT: B 168 PHE cc_start: 0.8012 (t80) cc_final: 0.7734 (t80) REVERT: B 388 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7696 (m110) REVERT: B 755 GLN cc_start: 0.8882 (pp30) cc_final: 0.8561 (pp30) REVERT: B 763 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8676 (tt) REVERT: B 985 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7891 (m-30) outliers start: 80 outliers final: 65 residues processed: 190 average time/residue: 0.1556 time to fit residues: 50.8569 Evaluate side-chains 184 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 113 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 100 optimal weight: 0.4980 chunk 304 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 3 optimal weight: 0.0050 chunk 221 optimal weight: 0.0270 chunk 147 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 overall best weight: 0.7056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 853 GLN C 907 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.106070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.073629 restraints weight = 83840.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.075112 restraints weight = 52226.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.076048 restraints weight = 32325.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.076379 restraints weight = 28523.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.076416 restraints weight = 24842.747| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3318 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= 0.119 Angle : 0.659 16.271 36786 Z= 0.313 Chirality : 0.046 0.269 4332 Planarity : 0.004 0.054 4650 Dihedral : 7.597 70.631 4816 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 2.55 % Allowed : 25.14 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.44 (0.15), residues: 3234 helix: 1.22 (0.21), residues: 638 sheet: -0.49 (0.20), residues: 609 loop : -1.97 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.017 0.001 TYR C 707 PHE 0.023 0.001 PHE C 168 TRP 0.028 0.002 TRP C 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00270 (26814) covalent geometry : angle 0.63059 (36525) SS BOND : bond 0.00431 ( 36) SS BOND : angle 1.60486 ( 72) hydrogen bonds : bond 0.03554 ( 805) hydrogen bonds : angle 5.41147 ( 2202) link_BETA1-4 : bond 0.01072 ( 21) link_BETA1-4 : angle 3.69195 ( 63) link_NAG-ASN : bond 0.00271 ( 42) link_NAG-ASN : angle 1.76990 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 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 194 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 122 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 498 ARG cc_start: 0.8292 (mmt-90) cc_final: 0.7797 (mmp80) REVERT: C 1141 LEU cc_start: 0.9145 (mt) cc_final: 0.8863 (pp) REVERT: A 211 ASN cc_start: 0.4254 (OUTLIER) cc_final: 0.2935 (t0) REVERT: A 456 PHE cc_start: 0.8458 (m-10) cc_final: 0.8230 (m-80) REVERT: A 464 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: A 835 LYS cc_start: 0.3510 (OUTLIER) cc_final: 0.2369 (pttm) REVERT: B 168 PHE cc_start: 0.7945 (t80) cc_final: 0.7673 (t80) REVERT: B 388 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7678 (m110) REVERT: B 755 GLN cc_start: 0.8863 (pp30) cc_final: 0.8581 (pp30) REVERT: B 763 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8586 (tt) REVERT: B 985 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7902 (m-30) outliers start: 72 outliers final: 55 residues processed: 185 average time/residue: 0.1454 time to fit residues: 46.7219 Evaluate side-chains 171 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 110 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 206 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 294 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 278 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 253 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 296 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN A 787 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.105626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.073088 restraints weight = 83645.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074618 restraints weight = 51468.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.075394 restraints weight = 32636.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075802 restraints weight = 28819.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075853 restraints weight = 24648.723| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26913 Z= 0.140 Angle : 0.671 15.847 36786 Z= 0.319 Chirality : 0.046 0.267 4332 Planarity : 0.004 0.054 4650 Dihedral : 7.496 69.705 4816 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.10 % Favored : 91.81 % Rotamer: Outliers : 2.66 % Allowed : 25.07 % Favored : 72.27 % 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: -1.46 (0.14), residues: 3234 helix: 1.09 (0.21), residues: 650 sheet: -0.43 (0.22), residues: 527 loop : -1.93 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.018 0.001 TYR A 873 PHE 0.022 0.001 PHE C 168 TRP 0.023 0.002 TRP C 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00323 (26814) covalent geometry : angle 0.64358 (36525) SS BOND : bond 0.00310 ( 36) SS BOND : angle 1.65391 ( 72) hydrogen bonds : bond 0.03595 ( 805) hydrogen bonds : angle 5.39935 ( 2202) link_BETA1-4 : bond 0.01039 ( 21) link_BETA1-4 : angle 3.66444 ( 63) link_NAG-ASN : bond 0.00270 ( 42) link_NAG-ASN : angle 1.76673 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4934.12 seconds wall clock time: 86 minutes 34.52 seconds (5194.52 seconds total)