Starting phenix.real_space_refine on Fri Mar 6 02:18:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z9r_14576/03_2026/7z9r_14576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9r_14576/03_2026/7z9r_14576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z9r_14576/03_2026/7z9r_14576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9r_14576/03_2026/7z9r_14576.map" model { file = "/net/cci-nas-00/data/ceres_data/7z9r_14576/03_2026/7z9r_14576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9r_14576/03_2026/7z9r_14576.cif" } resolution = 4.2 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= 0.000 sd= 0.003 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 120 5.16 5 C 17221 2.51 5 N 4415 2.21 5 O 5322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27078 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7719 Classifications: {'peptide': 988} Link IDs: {'PTRANS': 49, 'TRANS': 938} Chain breaks: 9 Chain: "B" Number of atoms: 7745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7745 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Chain: "C" Number of atoms: 7738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7738 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Z" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 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: 6.56, per 1000 atoms: 0.24 Number of scatterers: 27078 At special positions: 0 Unit cell: (130.784, 139.36, 216.544, 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 120 16.00 O 5322 8.00 N 4415 7.00 C 17221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.91 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.06 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=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.07 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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 Y 22 " - pdb=" SG CYS Y 96 " distance=2.01 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.01 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.01 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-ASN " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 709 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6246 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 55 sheets defined 24.5% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.981A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.335A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.540A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.237A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.941A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.599A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.025A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.339A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.040A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.874A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.583A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.296A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.762A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.518A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.594A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.809A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.966A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.355A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.574A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.642A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.371A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.680A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.527A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.944A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.111A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'Y' and resid 62 through 65 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 111 Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 111 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'Z' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.955A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.698A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.671A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.573A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.456A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.064A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.001A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.776A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.987A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.191A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.797A pdb=" N ILE A 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 'A' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.308A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.731A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.709A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.448A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.627A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.006A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 728 removed outlier: 5.988A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.777A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.344A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.699A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.556A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.669A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.917A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.550A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.882A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.977A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.001A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.712A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.166A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.574A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 3 through 8 Processing sheet with id=AF3, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.288A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG Y 38 " --> pdb=" O PHE Y 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.288A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 3 through 8 Processing sheet with id=AF6, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.293A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ARG X 38 " --> pdb=" O PHE X 47 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.293A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 3 through 8 Processing sheet with id=AF9, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.287A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG Z 38 " --> pdb=" O PHE Z 47 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.287A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3021 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: 7.85 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5965 1.33 - 1.46: 9667 1.46 - 1.59: 11885 1.59 - 1.72: 0 1.72 - 1.85: 153 Bond restraints: 27670 Sorted by residual: bond pdb=" C ASP C 138 " pdb=" N PRO C 139 " ideal model delta sigma weight residual 1.333 1.384 -0.051 1.17e-02 7.31e+03 1.89e+01 bond pdb=" C ASP A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 1.333 1.383 -0.050 1.17e-02 7.31e+03 1.84e+01 bond pdb=" CE1 HIS C1064 " pdb=" NE2 HIS C1064 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.57e+01 bond pdb=" N ASN A 81 " pdb=" CA ASN A 81 " ideal model delta sigma weight residual 1.458 1.533 -0.075 1.90e-02 2.77e+03 1.56e+01 bond pdb=" C ASN A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.331 1.381 -0.051 1.31e-02 5.83e+03 1.49e+01 ... (remaining 27665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 35532 2.72 - 5.44: 1958 5.44 - 8.16: 117 8.16 - 10.88: 15 10.88 - 13.60: 3 Bond angle restraints: 37625 Sorted by residual: angle pdb=" C CYS A 166 " pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sigma weight residual 112.05 99.52 12.53 1.52e+00 4.33e-01 6.79e+01 angle pdb=" C PHE C 329 " pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " ideal model delta sigma weight residual 109.22 120.23 -11.01 1.52e+00 4.33e-01 5.24e+01 angle pdb=" N SER B1147 " pdb=" CA SER B1147 " pdb=" CB SER B1147 " ideal model delta sigma weight residual 110.50 120.69 -10.19 1.70e+00 3.46e-01 3.60e+01 angle pdb=" N ASN B1108 " pdb=" CA ASN B1108 " pdb=" C ASN B1108 " ideal model delta sigma weight residual 111.82 118.77 -6.95 1.16e+00 7.43e-01 3.59e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 118.58 -5.98 1.00e+00 1.00e+00 3.58e+01 ... (remaining 37620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 16166 20.83 - 41.65: 848 41.65 - 62.48: 183 62.48 - 83.30: 53 83.30 - 104.13: 29 Dihedral angle restraints: 17279 sinusoidal: 7552 harmonic: 9727 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -174.98 88.98 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 171.46 -78.46 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 168.78 -75.78 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 17276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3793 0.144 - 0.288: 582 0.288 - 0.431: 51 0.431 - 0.575: 9 0.575 - 0.719: 2 Chirality restraints: 4437 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.07e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 2.02e+02 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 -2.12 -0.28 2.00e-02 2.50e+03 1.92e+02 ... (remaining 4434 not shown) Planarity restraints: 4808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " 0.363 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG P 1 " -0.094 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " -0.548 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.354 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG M 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1305 " -0.345 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG C1305 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG C1305 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG C1305 " 0.521 2.00e-02 2.50e+03 pdb=" O7 NAG C1305 " -0.099 2.00e-02 2.50e+03 ... (remaining 4805 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 1 1.93 - 2.67: 476 2.67 - 3.41: 35695 3.41 - 4.16: 67112 4.16 - 4.90: 116021 Nonbonded interactions: 219305 Sorted by model distance: nonbonded pdb=" OE1 GLU A 281 " pdb=" OD1 ASN A 282 " model vdw 1.182 3.040 nonbonded pdb=" SG CYS A 131 " pdb=" CA CYS A 166 " model vdw 1.927 3.064 nonbonded pdb=" O GLN B 613 " pdb=" OD1 ASP B 614 " model vdw 1.941 3.040 nonbonded pdb=" O THR A 333 " pdb=" OD1 ASN A 334 " model vdw 1.984 3.040 nonbonded pdb=" OD1 ASN C 137 " pdb=" N ASP C 138 " model vdw 2.047 3.120 ... (remaining 219300 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 263 or resid 265 through 676 or resid 690 through 827 \ or resid 856 through 1307)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 196 or resid 200 through 211 or resid 215 through 263 or resid 265 through 827 \ or resid 856 through 1307)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 196 or resid 200 through 211 or resid 215 through 1307 \ )) } 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' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.520 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.008 0.120 27774 Z= 0.524 Angle : 1.458 50.025 37895 Z= 0.910 Chirality : 0.105 0.719 4437 Planarity : 0.023 0.310 4766 Dihedral : 14.179 104.130 10907 Min Nonbonded Distance : 1.182 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 1.21 % Allowed : 4.62 % Favored : 94.17 % Cbeta Deviations : 0.48 % 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 are not related in a simple way. whole: -1.16 (0.13), residues: 3289 helix: -0.33 (0.19), residues: 678 sheet: -0.16 (0.17), residues: 798 loop : -1.21 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG C1091 TYR 0.058 0.007 TYR B 365 PHE 0.052 0.008 PHE B 565 TRP 0.037 0.006 TRP B 353 HIS 0.033 0.007 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00826 (27670) covalent geometry : angle 1.39512 (37625) SS BOND : bond 0.02332 ( 42) SS BOND : angle 6.31250 ( 84) hydrogen bonds : bond 0.14379 ( 1128) hydrogen bonds : angle 7.15917 ( 3021) link_BETA1-4 : bond 0.00370 ( 20) link_BETA1-4 : angle 1.55879 ( 60) link_NAG-ASN : bond 0.01287 ( 42) link_NAG-ASN : angle 5.50371 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 602 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7485 (p) REVERT: A 55 PHE cc_start: 0.8308 (m-80) cc_final: 0.7904 (m-80) REVERT: A 108 THR cc_start: 0.7057 (OUTLIER) cc_final: 0.6677 (t) REVERT: A 277 LEU cc_start: 0.8823 (mt) cc_final: 0.8622 (mm) REVERT: A 319 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7303 (mtp-110) REVERT: A 326 ILE cc_start: 0.7560 (mt) cc_final: 0.7229 (pt) REVERT: A 347 PHE cc_start: 0.7691 (m-80) cc_final: 0.6560 (m-80) REVERT: A 355 ARG cc_start: 0.6656 (ttm170) cc_final: 0.6228 (mtp85) REVERT: A 511 VAL cc_start: 0.6728 (t) cc_final: 0.6302 (m) REVERT: A 565 PHE cc_start: 0.8493 (p90) cc_final: 0.8241 (p90) REVERT: A 658 ASN cc_start: 0.8033 (m-40) cc_final: 0.7266 (t0) REVERT: A 666 ILE cc_start: 0.9133 (mt) cc_final: 0.8884 (mp) REVERT: A 758 SER cc_start: 0.8440 (m) cc_final: 0.8160 (p) REVERT: A 825 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7890 (mtmt) REVERT: A 1041 ASP cc_start: 0.9072 (m-30) cc_final: 0.8570 (t0) REVERT: A 1050 MET cc_start: 0.7821 (ptt) cc_final: 0.7434 (ptp) REVERT: A 1139 ASP cc_start: 0.8379 (t0) cc_final: 0.8013 (t0) REVERT: B 41 LYS cc_start: 0.6821 (mttm) cc_final: 0.6351 (mmtp) REVERT: B 53 ASP cc_start: 0.7882 (t0) cc_final: 0.7588 (t0) REVERT: B 223 LEU cc_start: 0.8527 (mp) cc_final: 0.8286 (mp) REVERT: B 266 TYR cc_start: 0.9034 (m-80) cc_final: 0.8564 (m-80) REVERT: B 347 PHE cc_start: 0.8055 (m-80) cc_final: 0.7494 (m-10) REVERT: B 389 ASP cc_start: 0.7927 (m-30) cc_final: 0.7406 (t0) REVERT: B 420 ASP cc_start: 0.8342 (m-30) cc_final: 0.8012 (m-30) REVERT: B 442 ASP cc_start: 0.7035 (m-30) cc_final: 0.6559 (m-30) REVERT: B 493 GLN cc_start: 0.7815 (tt0) cc_final: 0.7370 (tm-30) REVERT: B 532 ASN cc_start: 0.8336 (m-40) cc_final: 0.8117 (t0) REVERT: B 558 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7596 (mttt) REVERT: B 663 ASP cc_start: 0.9063 (t0) cc_final: 0.8775 (m-30) REVERT: B 698 SER cc_start: 0.8528 (t) cc_final: 0.7913 (p) REVERT: B 702 GLU cc_start: 0.8671 (tt0) cc_final: 0.8399 (tt0) REVERT: B 748 GLU cc_start: 0.7862 (mp0) cc_final: 0.7632 (mt-10) REVERT: B 825 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7681 (tptt) REVERT: B 868 GLU cc_start: 0.8385 (pt0) cc_final: 0.7714 (tm-30) REVERT: B 895 GLN cc_start: 0.9219 (pm20) cc_final: 0.8804 (pm20) REVERT: B 968 SER cc_start: 0.9343 (m) cc_final: 0.8584 (p) REVERT: B 997 ILE cc_start: 0.8870 (mt) cc_final: 0.8647 (mt) REVERT: B 1050 MET cc_start: 0.8613 (ptt) cc_final: 0.8396 (ptp) REVERT: B 1066 THR cc_start: 0.9589 (p) cc_final: 0.9328 (t) REVERT: B 1097 SER cc_start: 0.8757 (t) cc_final: 0.8399 (p) REVERT: C 44 ARG cc_start: 0.6981 (mtt90) cc_final: 0.6760 (mtt90) REVERT: C 88 ASP cc_start: 0.8095 (m-30) cc_final: 0.7551 (t70) REVERT: C 169 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7482 (mp0) REVERT: C 201 PHE cc_start: 0.7780 (t80) cc_final: 0.7576 (t80) REVERT: C 565 PHE cc_start: 0.8120 (p90) cc_final: 0.7916 (p90) REVERT: C 697 MET cc_start: 0.8831 (ptm) cc_final: 0.8522 (ptm) REVERT: C 773 GLU cc_start: 0.8322 (tt0) cc_final: 0.8087 (tp30) REVERT: C 780 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8830 (tp30) REVERT: C 819 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8348 (mt-10) REVERT: C 1100 THR cc_start: 0.7740 (p) cc_final: 0.7457 (p) REVERT: C 1101 HIS cc_start: 0.7453 (m90) cc_final: 0.7197 (m90) REVERT: C 1135 ASN cc_start: 0.5914 (t0) cc_final: 0.5455 (t0) REVERT: Y 36 TRP cc_start: 0.5928 (m100) cc_final: 0.5251 (m100) REVERT: Y 62 ASP cc_start: 0.6673 (m-30) cc_final: 0.6189 (p0) REVERT: Y 79 VAL cc_start: 0.7463 (p) cc_final: 0.6458 (m) REVERT: Y 88 TYR cc_start: 0.7292 (t80) cc_final: 0.6980 (m-10) REVERT: Y 105 LEU cc_start: 0.8029 (tp) cc_final: 0.7711 (tp) REVERT: Z 34 MET cc_start: 0.3444 (mmm) cc_final: 0.2728 (ppp) REVERT: Z 83 MET cc_start: -0.2953 (mtp) cc_final: -0.3187 (mtp) outliers start: 35 outliers final: 4 residues processed: 625 average time/residue: 0.1925 time to fit residues: 187.5809 Evaluate side-chains 257 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 251 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 81 ASN A 563 GLN A 564 GLN A 762 GLN A 784 GLN A 804 GLN A 935 GLN A 957 GLN A1011 GLN A1071 GLN B 234 ASN B 506 GLN B 519 HIS B 613 GLN B1048 HIS B1071 GLN C 81 ASN C 125 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 607 GLN C 655 HIS C 762 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN C1048 HIS Y 3 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104321 restraints weight = 62678.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101781 restraints weight = 60453.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102594 restraints weight = 50516.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103405 restraints weight = 40709.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103700 restraints weight = 35302.301| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 27774 Z= 0.144 Angle : 0.695 10.401 37895 Z= 0.340 Chirality : 0.048 0.285 4437 Planarity : 0.004 0.053 4766 Dihedral : 9.717 93.229 4986 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.21 % Allowed : 2.69 % Favored : 97.10 % 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 are not related in a simple way. whole: -0.21 (0.14), residues: 3289 helix: 0.92 (0.20), residues: 681 sheet: 0.13 (0.17), residues: 765 loop : -0.62 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1107 TYR 0.027 0.002 TYR C 369 PHE 0.037 0.002 PHE B 565 TRP 0.025 0.001 TRP C 64 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00312 (27670) covalent geometry : angle 0.66867 (37625) SS BOND : bond 0.00534 ( 42) SS BOND : angle 2.23378 ( 84) hydrogen bonds : bond 0.04686 ( 1128) hydrogen bonds : angle 5.79807 ( 3021) link_BETA1-4 : bond 0.00620 ( 20) link_BETA1-4 : angle 1.66684 ( 60) link_NAG-ASN : bond 0.00519 ( 42) link_NAG-ASN : angle 2.63994 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 387 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9107 (tp) cc_final: 0.8873 (tp) REVERT: A 101 ILE cc_start: 0.9133 (pt) cc_final: 0.8852 (tp) REVERT: A 347 PHE cc_start: 0.6449 (m-80) cc_final: 0.5738 (m-10) REVERT: A 365 TYR cc_start: 0.8171 (m-80) cc_final: 0.7822 (m-10) REVERT: A 387 LEU cc_start: 0.9069 (mp) cc_final: 0.8789 (mp) REVERT: A 699 LEU cc_start: 0.9058 (mt) cc_final: 0.8818 (mt) REVERT: A 1041 ASP cc_start: 0.7531 (m-30) cc_final: 0.7266 (t0) REVERT: B 41 LYS cc_start: 0.7468 (mttm) cc_final: 0.7248 (mttm) REVERT: B 188 ASN cc_start: 0.7757 (t0) cc_final: 0.7488 (m-40) REVERT: B 202 LYS cc_start: 0.7217 (tppt) cc_final: 0.6972 (tppt) REVERT: B 241 LEU cc_start: 0.7913 (mt) cc_final: 0.7643 (tp) REVERT: B 357 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7227 (mtp180) REVERT: B 508 TYR cc_start: 0.7755 (m-80) cc_final: 0.7073 (m-80) REVERT: B 558 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7446 (mttt) REVERT: B 708 SER cc_start: 0.9340 (p) cc_final: 0.8941 (m) REVERT: B 825 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8033 (tttt) REVERT: B 968 SER cc_start: 0.9497 (m) cc_final: 0.9104 (p) REVERT: B 1097 SER cc_start: 0.9250 (t) cc_final: 0.8766 (p) REVERT: C 204 TYR cc_start: 0.7687 (m-80) cc_final: 0.7357 (m-80) REVERT: C 533 LEU cc_start: 0.5997 (pp) cc_final: 0.5287 (mt) REVERT: C 734 THR cc_start: 0.9038 (m) cc_final: 0.8818 (t) REVERT: C 819 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8477 (mt-10) REVERT: C 900 MET cc_start: 0.8245 (mtp) cc_final: 0.7726 (mtm) REVERT: Y 94 TYR cc_start: 0.5007 (m-80) cc_final: 0.4627 (m-10) REVERT: Y 105 LEU cc_start: 0.8511 (tp) cc_final: 0.8217 (tp) outliers start: 6 outliers final: 4 residues processed: 392 average time/residue: 0.1634 time to fit residues: 105.8823 Evaluate side-chains 207 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 51 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 320 optimal weight: 30.0000 chunk 268 optimal weight: 0.9980 chunk 254 optimal weight: 0.0170 chunk 252 optimal weight: 0.9980 chunk 232 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 239 optimal weight: 0.4980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN A 926 GLN A1142 GLN B 239 GLN B 762 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.138617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099036 restraints weight = 61957.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098390 restraints weight = 53265.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098879 restraints weight = 40356.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099539 restraints weight = 33202.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099613 restraints weight = 29953.587| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27774 Z= 0.121 Angle : 0.618 10.371 37895 Z= 0.310 Chirality : 0.045 0.247 4437 Planarity : 0.004 0.046 4766 Dihedral : 8.215 82.635 4986 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: 0.14 (0.14), residues: 3289 helix: 1.41 (0.21), residues: 684 sheet: 0.21 (0.17), residues: 806 loop : -0.43 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.033 0.001 TYR A 904 PHE 0.024 0.001 PHE B 392 TRP 0.017 0.001 TRP C 64 HIS 0.010 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00263 (27670) covalent geometry : angle 0.59400 (37625) SS BOND : bond 0.00345 ( 42) SS BOND : angle 2.22292 ( 84) hydrogen bonds : bond 0.04210 ( 1128) hydrogen bonds : angle 5.47118 ( 3021) link_BETA1-4 : bond 0.00242 ( 20) link_BETA1-4 : angle 1.75164 ( 60) link_NAG-ASN : bond 0.00296 ( 42) link_NAG-ASN : angle 2.16440 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 320 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6555 (m-80) cc_final: 0.5813 (m-10) REVERT: A 365 TYR cc_start: 0.8132 (m-80) cc_final: 0.7817 (m-10) REVERT: A 387 LEU cc_start: 0.9127 (mp) cc_final: 0.8914 (mp) REVERT: A 598 ILE cc_start: 0.9102 (mt) cc_final: 0.8875 (pt) REVERT: A 658 ASN cc_start: 0.8317 (t0) cc_final: 0.8109 (t0) REVERT: A 699 LEU cc_start: 0.9085 (mt) cc_final: 0.8820 (mt) REVERT: B 30 ASN cc_start: 0.8693 (t0) cc_final: 0.8422 (m110) REVERT: B 508 TYR cc_start: 0.7636 (m-80) cc_final: 0.7397 (m-10) REVERT: B 558 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7313 (mttt) REVERT: B 825 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8085 (tppt) REVERT: B 968 SER cc_start: 0.9499 (m) cc_final: 0.9135 (p) REVERT: C 106 PHE cc_start: 0.7893 (m-80) cc_final: 0.7609 (m-80) REVERT: C 734 THR cc_start: 0.9073 (m) cc_final: 0.8855 (p) REVERT: C 819 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8519 (mt-10) REVERT: C 900 MET cc_start: 0.8025 (mtp) cc_final: 0.7743 (mtp) REVERT: Y 12 MET cc_start: 0.4649 (ttm) cc_final: 0.4060 (ttm) REVERT: Y 79 VAL cc_start: 0.7160 (p) cc_final: 0.6311 (m) REVERT: Y 94 TYR cc_start: 0.4491 (m-80) cc_final: 0.4052 (m-10) REVERT: Y 105 LEU cc_start: 0.8601 (tp) cc_final: 0.8362 (tp) outliers start: 4 outliers final: 2 residues processed: 324 average time/residue: 0.1635 time to fit residues: 87.7413 Evaluate side-chains 191 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 87 optimal weight: 0.7980 chunk 306 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN A 926 GLN A1010 GLN B 239 GLN B 519 HIS B 762 GLN B1011 GLN C 81 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.143925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104387 restraints weight = 62677.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103998 restraints weight = 46289.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104497 restraints weight = 37792.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104688 restraints weight = 33906.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104818 restraints weight = 28022.260| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27774 Z= 0.139 Angle : 0.597 12.776 37895 Z= 0.298 Chirality : 0.045 0.253 4437 Planarity : 0.004 0.047 4766 Dihedral : 7.240 74.664 4986 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3289 helix: 1.61 (0.21), residues: 663 sheet: 0.22 (0.17), residues: 804 loop : -0.39 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.022 0.001 TYR A1067 PHE 0.024 0.001 PHE B 275 TRP 0.014 0.001 TRP A 353 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00310 (27670) covalent geometry : angle 0.57570 (37625) SS BOND : bond 0.00822 ( 42) SS BOND : angle 2.00761 ( 84) hydrogen bonds : bond 0.04110 ( 1128) hydrogen bonds : angle 5.31660 ( 3021) link_BETA1-4 : bond 0.00228 ( 20) link_BETA1-4 : angle 1.85312 ( 60) link_NAG-ASN : bond 0.00271 ( 42) link_NAG-ASN : angle 1.98369 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6640 (m-80) cc_final: 0.5819 (m-10) REVERT: A 365 TYR cc_start: 0.8206 (m-80) cc_final: 0.7890 (m-10) REVERT: A 598 ILE cc_start: 0.9119 (mt) cc_final: 0.8795 (tt) REVERT: A 690 GLN cc_start: 0.6604 (mm-40) cc_final: 0.6186 (pm20) REVERT: A 698 SER cc_start: 0.9319 (t) cc_final: 0.8952 (p) REVERT: A 699 LEU cc_start: 0.9058 (mt) cc_final: 0.8769 (mt) REVERT: B 202 LYS cc_start: 0.7122 (mmtt) cc_final: 0.6036 (mptt) REVERT: B 558 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7423 (mttt) REVERT: B 825 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8162 (tttp) REVERT: B 968 SER cc_start: 0.9472 (m) cc_final: 0.9156 (p) REVERT: C 204 TYR cc_start: 0.7866 (m-80) cc_final: 0.7621 (m-80) REVERT: C 734 THR cc_start: 0.9122 (m) cc_final: 0.8910 (p) REVERT: C 819 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8593 (mt-10) REVERT: C 900 MET cc_start: 0.8303 (mtp) cc_final: 0.8096 (mtm) REVERT: Y 34 MET cc_start: 0.7066 (tpp) cc_final: 0.6239 (mtm) REVERT: Y 105 LEU cc_start: 0.8530 (tp) cc_final: 0.8187 (tp) REVERT: Z 34 MET cc_start: 0.1494 (mmt) cc_final: 0.1114 (ppp) outliers start: 3 outliers final: 0 residues processed: 288 average time/residue: 0.1642 time to fit residues: 79.6203 Evaluate side-chains 189 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 300 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 152 optimal weight: 0.5980 chunk 276 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 315 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 207 HIS B 218 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 563 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Y 84 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.138345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099730 restraints weight = 63495.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099080 restraints weight = 50120.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099743 restraints weight = 38850.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100011 restraints weight = 33203.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100134 restraints weight = 30412.676| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27774 Z= 0.215 Angle : 0.679 11.160 37895 Z= 0.340 Chirality : 0.048 0.273 4437 Planarity : 0.004 0.051 4766 Dihedral : 6.671 61.469 4986 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3289 helix: 1.45 (0.20), residues: 651 sheet: 0.30 (0.17), residues: 823 loop : -0.62 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1014 TYR 0.027 0.002 TYR A 904 PHE 0.020 0.002 PHE A 565 TRP 0.020 0.002 TRP Y 53 HIS 0.007 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00497 (27670) covalent geometry : angle 0.65787 (37625) SS BOND : bond 0.00418 ( 42) SS BOND : angle 2.15622 ( 84) hydrogen bonds : bond 0.04698 ( 1128) hydrogen bonds : angle 5.43901 ( 3021) link_BETA1-4 : bond 0.00376 ( 20) link_BETA1-4 : angle 1.94420 ( 60) link_NAG-ASN : bond 0.00420 ( 42) link_NAG-ASN : angle 2.11810 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6367 (m-80) cc_final: 0.5726 (m-10) REVERT: A 896 ILE cc_start: 0.9479 (tt) cc_final: 0.9146 (pt) REVERT: A 955 ASN cc_start: 0.9071 (m-40) cc_final: 0.8827 (t0) REVERT: B 41 LYS cc_start: 0.7616 (mmtm) cc_final: 0.7409 (mmtp) REVERT: B 202 LYS cc_start: 0.7359 (mmtt) cc_final: 0.7101 (mmtt) REVERT: B 465 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 468 ILE cc_start: 0.8864 (pt) cc_final: 0.8570 (mm) REVERT: B 558 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7238 (mttt) REVERT: B 968 SER cc_start: 0.9431 (m) cc_final: 0.9199 (p) REVERT: C 761 THR cc_start: 0.8663 (p) cc_final: 0.8439 (t) REVERT: C 900 MET cc_start: 0.8399 (mtp) cc_final: 0.8160 (mtp) REVERT: Y 79 VAL cc_start: 0.7349 (p) cc_final: 0.6607 (m) outliers start: 1 outliers final: 1 residues processed: 268 average time/residue: 0.1635 time to fit residues: 72.3831 Evaluate side-chains 174 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 166 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 310 optimal weight: 0.0670 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 0.0670 chunk 297 optimal weight: 0.1980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN B 207 HIS B 762 GLN B 992 GLN C 81 ASN C 901 GLN ** C 954 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 = 0.3861 r_free = 0.3861 target = 0.137326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099591 restraints weight = 62053.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098533 restraints weight = 62395.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099069 restraints weight = 49378.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099633 restraints weight = 40976.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099924 restraints weight = 35941.492| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27774 Z= 0.107 Angle : 0.574 10.107 37895 Z= 0.288 Chirality : 0.044 0.241 4437 Planarity : 0.004 0.054 4766 Dihedral : 5.908 60.475 4986 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.07 % Allowed : 1.17 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3289 helix: 1.69 (0.21), residues: 659 sheet: 0.45 (0.17), residues: 829 loop : -0.51 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.021 0.001 TYR A 904 PHE 0.027 0.001 PHE B 906 TRP 0.024 0.001 TRP C 64 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00231 (27670) covalent geometry : angle 0.55449 (37625) SS BOND : bond 0.00354 ( 42) SS BOND : angle 2.19523 ( 84) hydrogen bonds : bond 0.03889 ( 1128) hydrogen bonds : angle 5.24646 ( 3021) link_BETA1-4 : bond 0.00277 ( 20) link_BETA1-4 : angle 1.73188 ( 60) link_NAG-ASN : bond 0.00220 ( 42) link_NAG-ASN : angle 1.65199 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 293 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6045 (m-80) cc_final: 0.5545 (m-10) REVERT: A 495 TYR cc_start: 0.4939 (m-80) cc_final: 0.4329 (m-80) REVERT: A 540 ASN cc_start: 0.7535 (t0) cc_final: 0.7319 (t0) REVERT: A 690 GLN cc_start: 0.6655 (mm-40) cc_final: 0.6185 (pm20) REVERT: A 699 LEU cc_start: 0.8889 (mt) cc_final: 0.8629 (mp) REVERT: A 896 ILE cc_start: 0.9434 (tt) cc_final: 0.9062 (pt) REVERT: A 955 ASN cc_start: 0.8962 (m-40) cc_final: 0.8628 (t0) REVERT: B 202 LYS cc_start: 0.7471 (mmtt) cc_final: 0.6551 (mmmt) REVERT: B 517 LEU cc_start: 0.7244 (mm) cc_final: 0.6578 (mm) REVERT: B 549 THR cc_start: 0.8959 (m) cc_final: 0.8711 (p) REVERT: B 558 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7440 (mmtt) REVERT: B 775 ASP cc_start: 0.7910 (t0) cc_final: 0.7675 (t70) REVERT: B 962 LEU cc_start: 0.9174 (tp) cc_final: 0.8943 (tp) REVERT: B 968 SER cc_start: 0.9430 (m) cc_final: 0.9203 (p) REVERT: B 1127 ASP cc_start: 0.7499 (m-30) cc_final: 0.7287 (t0) REVERT: C 734 THR cc_start: 0.9139 (m) cc_final: 0.8905 (p) REVERT: Y 34 MET cc_start: 0.6929 (tpp) cc_final: 0.6091 (mtm) REVERT: Y 79 VAL cc_start: 0.7261 (p) cc_final: 0.6471 (p) REVERT: Z 12 MET cc_start: -0.2624 (mtt) cc_final: -0.3404 (tpp) REVERT: Z 34 MET cc_start: 0.2748 (pmm) cc_final: 0.2485 (mmt) outliers start: 2 outliers final: 0 residues processed: 294 average time/residue: 0.1573 time to fit residues: 76.7944 Evaluate side-chains 180 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 15 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 111 optimal weight: 0.2980 chunk 188 optimal weight: 0.0870 chunk 187 optimal weight: 0.1980 chunk 313 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN A 784 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 954 GLN C1005 GLN Y 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.140345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101633 restraints weight = 61522.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100334 restraints weight = 64213.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101126 restraints weight = 53958.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101398 restraints weight = 45847.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101895 restraints weight = 37820.529| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27774 Z= 0.104 Angle : 0.567 11.927 37895 Z= 0.284 Chirality : 0.044 0.213 4437 Planarity : 0.004 0.057 4766 Dihedral : 5.432 56.101 4986 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.07 % Allowed : 0.59 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3289 helix: 1.85 (0.21), residues: 647 sheet: 0.53 (0.17), residues: 847 loop : -0.44 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 403 TYR 0.023 0.001 TYR A 904 PHE 0.029 0.001 PHE A 497 TRP 0.017 0.001 TRP Y 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00226 (27670) covalent geometry : angle 0.54925 (37625) SS BOND : bond 0.00293 ( 42) SS BOND : angle 1.98338 ( 84) hydrogen bonds : bond 0.03746 ( 1128) hydrogen bonds : angle 5.16091 ( 3021) link_BETA1-4 : bond 0.00215 ( 20) link_BETA1-4 : angle 1.76811 ( 60) link_NAG-ASN : bond 0.00175 ( 42) link_NAG-ASN : angle 1.54040 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6659 (m-80) cc_final: 0.5999 (m-10) REVERT: A 393 THR cc_start: 0.8210 (p) cc_final: 0.7992 (t) REVERT: A 540 ASN cc_start: 0.7526 (t0) cc_final: 0.7309 (t0) REVERT: A 690 GLN cc_start: 0.6656 (mm-40) cc_final: 0.6202 (pm20) REVERT: A 699 LEU cc_start: 0.8823 (mt) cc_final: 0.8585 (mp) REVERT: A 896 ILE cc_start: 0.9388 (tt) cc_final: 0.9005 (pt) REVERT: A 955 ASN cc_start: 0.8935 (m-40) cc_final: 0.8694 (t0) REVERT: B 54 LEU cc_start: 0.8350 (tp) cc_final: 0.7592 (tp) REVERT: B 202 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6419 (mmmt) REVERT: B 420 ASP cc_start: 0.7079 (m-30) cc_final: 0.6878 (m-30) REVERT: B 508 TYR cc_start: 0.7348 (m-80) cc_final: 0.6778 (m-80) REVERT: B 517 LEU cc_start: 0.7282 (mm) cc_final: 0.6661 (mm) REVERT: B 549 THR cc_start: 0.8986 (m) cc_final: 0.8752 (p) REVERT: B 558 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7408 (mttt) REVERT: B 775 ASP cc_start: 0.7867 (t0) cc_final: 0.7645 (t70) REVERT: B 968 SER cc_start: 0.9447 (m) cc_final: 0.9245 (p) REVERT: C 204 TYR cc_start: 0.7846 (m-80) cc_final: 0.7615 (m-80) REVERT: C 313 TYR cc_start: 0.8823 (m-80) cc_final: 0.8581 (m-80) REVERT: C 734 THR cc_start: 0.9123 (m) cc_final: 0.8916 (p) REVERT: C 901 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8756 (tp40) REVERT: C 1100 THR cc_start: 0.8179 (p) cc_final: 0.7950 (p) REVERT: Y 34 MET cc_start: 0.7070 (tpp) cc_final: 0.6300 (mtm) REVERT: Z 12 MET cc_start: -0.2787 (mtt) cc_final: -0.3511 (tpp) REVERT: Z 34 MET cc_start: 0.2723 (pmm) cc_final: 0.1880 (ttm) outliers start: 2 outliers final: 0 residues processed: 276 average time/residue: 0.1546 time to fit residues: 71.7438 Evaluate side-chains 180 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 136 optimal weight: 0.0870 chunk 311 optimal weight: 30.0000 chunk 229 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 207 HIS A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B1088 HIS C 81 ASN C 450 ASN C 804 GLN C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096227 restraints weight = 62892.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094127 restraints weight = 62826.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.094748 restraints weight = 57247.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094848 restraints weight = 50088.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095388 restraints weight = 39734.580| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 27774 Z= 0.268 Angle : 0.741 12.361 37895 Z= 0.372 Chirality : 0.049 0.241 4437 Planarity : 0.005 0.063 4766 Dihedral : 6.208 45.941 4986 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 1.07 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3289 helix: 1.05 (0.20), residues: 635 sheet: 0.30 (0.17), residues: 846 loop : -0.68 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 454 TYR 0.026 0.002 TYR A 495 PHE 0.024 0.002 PHE A1095 TRP 0.018 0.002 TRP B 104 HIS 0.008 0.002 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00626 (27670) covalent geometry : angle 0.72032 (37625) SS BOND : bond 0.00452 ( 42) SS BOND : angle 2.25829 ( 84) hydrogen bonds : bond 0.05079 ( 1128) hydrogen bonds : angle 5.63310 ( 3021) link_BETA1-4 : bond 0.00322 ( 20) link_BETA1-4 : angle 2.00776 ( 60) link_NAG-ASN : bond 0.00546 ( 42) link_NAG-ASN : angle 2.18152 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6655 (m-80) cc_final: 0.6042 (m-10) REVERT: A 393 THR cc_start: 0.8383 (p) cc_final: 0.8174 (t) REVERT: A 896 ILE cc_start: 0.9486 (tt) cc_final: 0.9219 (pt) REVERT: B 54 LEU cc_start: 0.8536 (tp) cc_final: 0.7817 (tp) REVERT: B 549 THR cc_start: 0.9114 (m) cc_final: 0.8902 (p) REVERT: B 558 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7505 (mttt) REVERT: C 564 GLN cc_start: 0.7054 (mt0) cc_final: 0.6650 (mt0) REVERT: Y 2 VAL cc_start: 0.5497 (t) cc_final: 0.5229 (m) REVERT: Y 79 VAL cc_start: 0.7463 (p) cc_final: 0.6504 (m) REVERT: Z 34 MET cc_start: 0.3114 (pmm) cc_final: 0.2276 (ttm) outliers start: 2 outliers final: 1 residues processed: 237 average time/residue: 0.1612 time to fit residues: 64.0405 Evaluate side-chains 159 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 199 optimal weight: 1.9990 chunk 287 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN B 125 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS C 87 ASN C 493 GLN C 544 ASN C 901 GLN C 955 ASN C 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.098850 restraints weight = 60776.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096006 restraints weight = 61599.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096850 restraints weight = 49936.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.097356 restraints weight = 40426.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097994 restraints weight = 35690.478| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27774 Z= 0.130 Angle : 0.599 10.991 37895 Z= 0.304 Chirality : 0.045 0.213 4437 Planarity : 0.004 0.060 4766 Dihedral : 5.652 42.116 4986 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3289 helix: 1.43 (0.21), residues: 635 sheet: 0.39 (0.17), residues: 858 loop : -0.65 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 19 TYR 0.028 0.001 TYR A 904 PHE 0.040 0.001 PHE B 275 TRP 0.016 0.001 TRP Y 36 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00299 (27670) covalent geometry : angle 0.58241 (37625) SS BOND : bond 0.00272 ( 42) SS BOND : angle 1.96714 ( 84) hydrogen bonds : bond 0.04219 ( 1128) hydrogen bonds : angle 5.40712 ( 3021) link_BETA1-4 : bond 0.00281 ( 20) link_BETA1-4 : angle 1.65881 ( 60) link_NAG-ASN : bond 0.00244 ( 42) link_NAG-ASN : angle 1.67967 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6119 (m-80) cc_final: 0.5653 (m-10) REVERT: A 428 ASP cc_start: 0.7596 (p0) cc_final: 0.6973 (t0) REVERT: A 896 ILE cc_start: 0.9409 (tt) cc_final: 0.9156 (pt) REVERT: A 1041 ASP cc_start: 0.6897 (t70) cc_final: 0.6674 (t0) REVERT: B 54 LEU cc_start: 0.8038 (tp) cc_final: 0.7330 (tp) REVERT: B 558 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7452 (mttt) REVERT: C 564 GLN cc_start: 0.7081 (mt0) cc_final: 0.6674 (mt0) REVERT: C 618 THR cc_start: 0.8547 (p) cc_final: 0.8160 (t) REVERT: Y 12 MET cc_start: 0.4303 (tpt) cc_final: 0.3974 (mmm) REVERT: Y 34 MET cc_start: 0.7321 (tpp) cc_final: 0.6340 (mtt) REVERT: Y 64 VAL cc_start: 0.7107 (m) cc_final: 0.6714 (m) REVERT: Z 12 MET cc_start: -0.2492 (mtt) cc_final: -0.3157 (tpp) REVERT: Z 34 MET cc_start: 0.2983 (pmm) cc_final: 0.2693 (ttp) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1714 time to fit residues: 68.7746 Evaluate side-chains 160 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 156 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 chunk 115 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 325 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS C 81 ASN C 544 ASN C 901 GLN C 965 GLN Y 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100528 restraints weight = 63473.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100237 restraints weight = 49806.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100695 restraints weight = 41725.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100851 restraints weight = 38827.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101383 restraints weight = 30961.337| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27774 Z= 0.168 Angle : 0.615 10.684 37895 Z= 0.310 Chirality : 0.046 0.290 4437 Planarity : 0.004 0.065 4766 Dihedral : 5.601 39.220 4986 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.07 % Allowed : 0.45 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3289 helix: 1.27 (0.21), residues: 650 sheet: 0.34 (0.17), residues: 840 loop : -0.64 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 509 TYR 0.029 0.001 TYR A 904 PHE 0.023 0.002 PHE C 906 TRP 0.017 0.001 TRP Y 36 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00394 (27670) covalent geometry : angle 0.59804 (37625) SS BOND : bond 0.00339 ( 42) SS BOND : angle 1.86298 ( 84) hydrogen bonds : bond 0.04304 ( 1128) hydrogen bonds : angle 5.42394 ( 3021) link_BETA1-4 : bond 0.00170 ( 20) link_BETA1-4 : angle 1.69754 ( 60) link_NAG-ASN : bond 0.00280 ( 42) link_NAG-ASN : angle 1.77275 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7328 (ptt180) cc_final: 0.7094 (mtm180) REVERT: A 347 PHE cc_start: 0.6183 (m-80) cc_final: 0.5682 (m-10) REVERT: A 428 ASP cc_start: 0.7640 (p0) cc_final: 0.7013 (t0) REVERT: A 1041 ASP cc_start: 0.6967 (t70) cc_final: 0.6682 (t0) REVERT: B 54 LEU cc_start: 0.8338 (tp) cc_final: 0.7549 (tp) REVERT: B 558 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7576 (mttt) REVERT: C 84 LEU cc_start: 0.8451 (mm) cc_final: 0.8250 (mm) REVERT: C 564 GLN cc_start: 0.7051 (mt0) cc_final: 0.6592 (mt0) REVERT: C 618 THR cc_start: 0.8561 (p) cc_final: 0.8232 (t) REVERT: Y 12 MET cc_start: 0.4008 (tpt) cc_final: 0.3675 (mmm) REVERT: Y 34 MET cc_start: 0.7443 (tpp) cc_final: 0.6354 (mtt) REVERT: Y 83 MET cc_start: 0.5764 (pmm) cc_final: 0.5176 (pmm) outliers start: 2 outliers final: 1 residues processed: 234 average time/residue: 0.1597 time to fit residues: 62.6985 Evaluate side-chains 159 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 287 optimal weight: 0.5980 chunk 254 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 238 optimal weight: 20.0000 chunk 157 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS C 544 ASN C 901 GLN C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101768 restraints weight = 63085.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100749 restraints weight = 54860.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101369 restraints weight = 41833.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101779 restraints weight = 34816.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101996 restraints weight = 31376.740| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27774 Z= 0.120 Angle : 0.577 10.283 37895 Z= 0.292 Chirality : 0.045 0.230 4437 Planarity : 0.004 0.062 4766 Dihedral : 5.331 39.573 4986 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.62 % 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 are not related in a simple way. whole: 0.14 (0.14), residues: 3289 helix: 1.49 (0.21), residues: 650 sheet: 0.50 (0.17), residues: 820 loop : -0.60 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1014 TYR 0.025 0.001 TYR A 904 PHE 0.028 0.001 PHE Y 68 TRP 0.017 0.001 TRP Y 36 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00274 (27670) covalent geometry : angle 0.55996 (37625) SS BOND : bond 0.00345 ( 42) SS BOND : angle 1.96886 ( 84) hydrogen bonds : bond 0.03953 ( 1128) hydrogen bonds : angle 5.31070 ( 3021) link_BETA1-4 : bond 0.00243 ( 20) link_BETA1-4 : angle 1.60562 ( 60) link_NAG-ASN : bond 0.00206 ( 42) link_NAG-ASN : angle 1.59455 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3910.08 seconds wall clock time: 68 minutes 48.23 seconds (4128.23 seconds total)