Starting phenix.real_space_refine on Tue Aug 26 23:38:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhe_60100/08_2025/8zhe_60100.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhe_60100/08_2025/8zhe_60100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zhe_60100/08_2025/8zhe_60100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhe_60100/08_2025/8zhe_60100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zhe_60100/08_2025/8zhe_60100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhe_60100/08_2025/8zhe_60100.map" } resolution = 3.16 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= 0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9249 atoms to isotropic. 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 147 5.16 5 C 22506 2.51 5 N 5841 2.21 5 O 7047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35541 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8320 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8320 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 8320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8320 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1656 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "L" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1591 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1656 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "G" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1591 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1656 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "K" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1591 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.28, per 1000 atoms: 0.18 Number of scatterers: 35541 At special positions: 0 Unit cell: (191.632, 194.37, 199.845, 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 147 16.00 O 7047 8.00 N 5841 7.00 C 22506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 145 " - pdb=" SG CYS L 204 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 145 " - pdb=" SG CYS G 204 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 91 " distance=2.03 Simple disulfide: pdb=" SG CYS K 145 " - pdb=" SG CYS K 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 343 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8376 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 83 sheets defined 17.3% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.660A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.761A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.271A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.941A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.762A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.502A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.502A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.559A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.900A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.596A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.740A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.775A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.272A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.153A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.730A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.721A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 916 " --> pdb=" O GLN B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 916' Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.903A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.247A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.823A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.461A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.825A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.718A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.267A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.842A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.718A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.046A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.765A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.860A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.939A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.851A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.990A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 192 through 196 Processing helix chain 'L' and resid 132 through 137 Processing helix chain 'L' and resid 192 through 198 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.874A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 165 No H-bonds generated for 'chain 'F' and resid 163 through 165' Processing helix chain 'F' and resid 192 through 196 Processing helix chain 'G' and resid 132 through 137 Processing helix chain 'G' and resid 192 through 198 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.521A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'J' and resid 163 through 165 No H-bonds generated for 'chain 'J' and resid 163 through 165' Processing helix chain 'J' and resid 192 through 196 Processing helix chain 'K' and resid 132 through 137 Processing helix chain 'K' and resid 192 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.746A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.560A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.492A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.708A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.555A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.294A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.630A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.560A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.897A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.633A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.216A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.755A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.627A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.235A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.930A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.525A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 156 removed outlier: 6.373A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.569A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.116A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.550A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.163A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.641A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 583 through 586 removed outlier: 7.121A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.384A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.580A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.580A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.394A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 49 through 55 removed outlier: 4.009A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.512A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.873A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 152 through 158 removed outlier: 6.543A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.998A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.586A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.537A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.630A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.302A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.870A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.537A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.235A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.605A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.753A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.038A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 127 through 129 removed outlier: 3.530A pdb=" N CYS H 147 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP H 151 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 127 through 129 removed outlier: 3.530A pdb=" N CYS H 147 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP H 151 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 158 through 161 Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.573A pdb=" N VAL L 18 " --> pdb=" O ILE L 78 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.986A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP L 88 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 100 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.986A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP L 88 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.735A pdb=" N PHE L 129 " --> pdb=" O VAL L 144 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL L 144 " --> pdb=" O PHE L 129 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR L 183 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.735A pdb=" N PHE L 129 " --> pdb=" O VAL L 144 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL L 144 " --> pdb=" O PHE L 129 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR L 183 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 156 through 160 removed outlier: 3.545A pdb=" N SER L 211 " --> pdb=" O HIS L 208 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 156 through 160 Processing sheet with id=AG9, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.692A pdb=" N SER F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 73 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.043A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 94 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR F 114 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.572A pdb=" N CYS F 147 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP F 151 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR F 183 " --> pdb=" O ASP F 151 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.572A pdb=" N CYS F 147 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP F 151 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR F 183 " --> pdb=" O ASP F 151 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AH5, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AH6, first strand: chain 'G' and resid 46 through 49 removed outlier: 6.840A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP G 88 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL G 100 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.853A pdb=" N PHE G 129 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA G 141 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU G 191 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.853A pdb=" N PHE G 129 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA G 141 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU G 191 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 156 through 160 removed outlier: 3.643A pdb=" N CYS G 204 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS G 215 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER G 211 " --> pdb=" O HIS G 208 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.523A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP J 73 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 58 through 60 removed outlier: 5.031A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR J 94 " --> pdb=" O THR J 114 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR J 114 " --> pdb=" O TYR J 94 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.563A pdb=" N CYS J 147 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP J 151 " --> pdb=" O TYR J 183 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.563A pdb=" N CYS J 147 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP J 151 " --> pdb=" O TYR J 183 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 158 through 161 Processing sheet with id=AI6, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AI7, first strand: chain 'K' and resid 45 through 49 removed outlier: 6.835A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 45 through 49 removed outlier: 6.835A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.580A pdb=" N ALA K 141 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.580A pdb=" N ALA K 141 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 156 through 160 removed outlier: 3.564A pdb=" N SER K 211 " --> pdb=" O HIS K 208 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3462 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: 9.26 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11348 1.35 - 1.48: 9601 1.48 - 1.61: 15231 1.61 - 1.74: 0 1.74 - 1.87: 186 Bond restraints: 36366 Sorted by residual: bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.38e-02 5.25e+03 9.83e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" N ASN B 234 " pdb=" CA ASN B 234 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.27e-02 6.20e+03 4.11e+00 bond pdb=" N ASN A 234 " pdb=" CA ASN A 234 " ideal model delta sigma weight residual 1.455 1.478 -0.023 1.22e-02 6.72e+03 3.50e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.32e+00 ... (remaining 36361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 48614 2.08 - 4.17: 816 4.17 - 6.25: 88 6.25 - 8.34: 29 8.34 - 10.42: 7 Bond angle restraints: 49554 Sorted by residual: angle pdb=" CA LYS G 140 " pdb=" CB LYS G 140 " pdb=" CG LYS G 140 " ideal model delta sigma weight residual 114.10 122.03 -7.93 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N ALA G 87 " pdb=" CA ALA G 87 " pdb=" C ALA G 87 " ideal model delta sigma weight residual 107.88 113.46 -5.58 1.41e+00 5.03e-01 1.57e+01 angle pdb=" CA ARG H 19 " pdb=" CB ARG H 19 " pdb=" CG ARG H 19 " ideal model delta sigma weight residual 114.10 121.95 -7.85 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CB GLN A1142 " pdb=" CG GLN A1142 " pdb=" CD GLN A1142 " ideal model delta sigma weight residual 112.60 119.15 -6.55 1.70e+00 3.46e-01 1.48e+01 angle pdb=" CB GLN F 82 " pdb=" CG GLN F 82 " pdb=" CD GLN F 82 " ideal model delta sigma weight residual 112.60 119.05 -6.45 1.70e+00 3.46e-01 1.44e+01 ... (remaining 49549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 19568 17.94 - 35.89: 2211 35.89 - 53.83: 517 53.83 - 71.77: 98 71.77 - 89.71: 34 Dihedral angle restraints: 22428 sinusoidal: 9378 harmonic: 13050 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -169.37 83.37 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -169.01 83.01 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -165.73 79.73 1 1.00e+01 1.00e-02 7.89e+01 ... (remaining 22425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 5761 0.160 - 0.320: 9 0.320 - 0.480: 3 0.480 - 0.640: 1 0.640 - 0.800: 1 Chirality restraints: 5775 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.03e+01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.92e+00 ... (remaining 5772 not shown) Planarity restraints: 6387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.098 2.00e-02 2.50e+03 8.04e-02 8.07e+01 pdb=" C7 NAG D 1 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.074 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.127 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.079 2.00e-02 2.50e+03 6.48e-02 5.25e+01 pdb=" C7 NAG D 2 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 139 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.058 5.00e-02 4.00e+02 ... (remaining 6384 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 205 2.52 - 3.12: 24562 3.12 - 3.71: 53521 3.71 - 4.31: 71884 4.31 - 4.90: 122569 Nonbonded interactions: 272741 Sorted by model distance: nonbonded pdb=" CD ARG G 40 " pdb=" OD1 ASP G 85 " model vdw 1.931 3.440 nonbonded pdb=" NE ARG G 40 " pdb=" OD1 ASP G 85 " model vdw 2.200 3.120 nonbonded pdb=" O VAL B 401 " pdb=" OH TYR B 451 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.249 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.265 3.040 ... (remaining 272736 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.920 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 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 : 0.003 0.057 36480 Z= 0.172 Angle : 0.659 13.660 49842 Z= 0.329 Chirality : 0.048 0.800 5775 Planarity : 0.005 0.108 6342 Dihedral : 15.436 89.713 13890 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.72 % Allowed : 23.72 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.12), residues: 4449 helix: 0.41 (0.20), residues: 681 sheet: 0.60 (0.15), residues: 1227 loop : -1.77 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.021 0.001 TYR H 109 PHE 0.017 0.001 PHE A 238 TRP 0.058 0.001 TRP F 110 HIS 0.012 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00346 (36366) covalent geometry : angle 0.63761 (49554) SS BOND : bond 0.00247 ( 54) SS BOND : angle 0.98288 ( 108) hydrogen bonds : bond 0.24012 ( 1183) hydrogen bonds : angle 9.11938 ( 3462) link_BETA1-4 : bond 0.00463 ( 15) link_BETA1-4 : angle 0.93512 ( 45) link_NAG-ASN : bond 0.00614 ( 45) link_NAG-ASN : angle 3.16832 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 1.316 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 384 PRO cc_start: 0.6657 (Cg_endo) cc_final: 0.6128 (Cg_exo) REVERT: A 740 MET cc_start: 0.6457 (mmm) cc_final: 0.5386 (mmm) REVERT: A 869 MET cc_start: 0.7960 (mmm) cc_final: 0.7393 (mtt) REVERT: A 1050 MET cc_start: 0.8228 (ptm) cc_final: 0.7963 (ptp) REVERT: B 215 ASP cc_start: 0.7556 (t0) cc_final: 0.7209 (t70) REVERT: B 869 MET cc_start: 0.7642 (mmm) cc_final: 0.6814 (mtt) REVERT: C 84 LEU cc_start: 0.6504 (mt) cc_final: 0.5735 (mp) REVERT: C 177 MET cc_start: -0.1811 (mtt) cc_final: -0.4960 (ttm) REVERT: C 329 PHE cc_start: 0.7780 (m-80) cc_final: 0.7296 (m-10) REVERT: C 823 PHE cc_start: 0.7339 (t80) cc_final: 0.6882 (m-80) REVERT: C 869 MET cc_start: 0.8114 (mmm) cc_final: 0.7874 (mmm) REVERT: C 962 LEU cc_start: 0.7845 (tp) cc_final: 0.7608 (tp) REVERT: H 3 GLN cc_start: 0.9527 (mm110) cc_final: 0.9248 (mp10) REVERT: H 34 MET cc_start: 0.7648 (mmt) cc_final: 0.7442 (mmm) REVERT: H 183 TYR cc_start: 0.8550 (m-80) cc_final: 0.8047 (m-80) REVERT: H 209 PRO cc_start: 0.3833 (Cg_exo) cc_final: 0.3587 (Cg_endo) REVERT: L 38 GLN cc_start: 0.1586 (OUTLIER) cc_final: 0.1379 (tt0) REVERT: L 191 LEU cc_start: 0.2893 (tp) cc_final: 0.2369 (mt) REVERT: K 207 THR cc_start: 0.4004 (m) cc_final: 0.3701 (m) outliers start: 28 outliers final: 9 residues processed: 329 average time/residue: 0.1761 time to fit residues: 98.7571 Evaluate side-chains 182 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 85 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.0770 chunk 424 optimal weight: 5.9990 overall best weight: 1.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 196 ASN A1005 GLN B 532 ASN B 544 ASN B 751 ASN B 901 GLN B1142 GLN C 66 HIS C 542 ASN C 957 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 HIS F 100 GLN G 195 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.165963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.113565 restraints weight = 105163.657| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 4.86 r_work: 0.3357 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36480 Z= 0.169 Angle : 0.635 16.045 49842 Z= 0.319 Chirality : 0.046 0.448 5775 Planarity : 0.005 0.076 6342 Dihedral : 5.519 56.500 6085 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.86 % Allowed : 21.54 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.12), residues: 4449 helix: 0.83 (0.20), residues: 711 sheet: 0.76 (0.15), residues: 1149 loop : -1.71 (0.11), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 40 TYR 0.021 0.002 TYR L 37 PHE 0.023 0.002 PHE C 43 TRP 0.016 0.001 TRP F 110 HIS 0.010 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00385 (36366) covalent geometry : angle 0.61709 (49554) SS BOND : bond 0.00236 ( 54) SS BOND : angle 1.21378 ( 108) hydrogen bonds : bond 0.04287 ( 1183) hydrogen bonds : angle 6.07824 ( 3462) link_BETA1-4 : bond 0.00411 ( 15) link_BETA1-4 : angle 1.17412 ( 45) link_NAG-ASN : bond 0.00472 ( 45) link_NAG-ASN : angle 2.74766 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 189 time to evaluate : 1.075 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 242 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7112 (mm) REVERT: A 392 PHE cc_start: 0.8033 (m-80) cc_final: 0.7667 (t80) REVERT: A 394 ASN cc_start: 0.7073 (OUTLIER) cc_final: 0.6384 (m110) REVERT: A 451 TYR cc_start: 0.5262 (t80) cc_final: 0.4842 (t80) REVERT: A 740 MET cc_start: 0.7131 (mmm) cc_final: 0.6785 (mmm) REVERT: A 823 PHE cc_start: 0.8205 (t80) cc_final: 0.7842 (m-80) REVERT: A 869 MET cc_start: 0.8815 (mmm) cc_final: 0.8379 (mtt) REVERT: B 58 PHE cc_start: 0.7455 (m-10) cc_final: 0.7086 (m-10) REVERT: B 136 CYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6857 (p) REVERT: B 197 ILE cc_start: 0.9128 (pp) cc_final: 0.8821 (pp) REVERT: B 215 ASP cc_start: 0.7257 (t0) cc_final: 0.6819 (t0) REVERT: B 242 LEU cc_start: 0.7032 (mm) cc_final: 0.6707 (mt) REVERT: B 902 MET cc_start: 0.8278 (tpt) cc_final: 0.8076 (mmm) REVERT: B 990 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: B 1142 GLN cc_start: 0.9354 (tt0) cc_final: 0.8909 (tp40) REVERT: B 1145 LEU cc_start: 0.8061 (mt) cc_final: 0.7353 (tt) REVERT: C 153 MET cc_start: 0.6490 (ppp) cc_final: 0.6184 (ppp) REVERT: C 177 MET cc_start: -0.0825 (mtt) cc_final: -0.4815 (ttm) REVERT: C 286 THR cc_start: 0.8433 (m) cc_final: 0.8136 (p) REVERT: C 329 PHE cc_start: 0.7837 (m-80) cc_final: 0.7596 (m-80) REVERT: C 396 TYR cc_start: 0.8828 (m-80) cc_final: 0.8504 (m-80) REVERT: C 731 MET cc_start: 0.8490 (ptt) cc_final: 0.7996 (ptt) REVERT: C 780 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8308 (mm-30) REVERT: C 786 LYS cc_start: 0.8208 (tppt) cc_final: 0.7976 (tppt) REVERT: C 823 PHE cc_start: 0.8047 (t80) cc_final: 0.7366 (m-80) REVERT: H 3 GLN cc_start: 0.9337 (mm110) cc_final: 0.9062 (mp10) REVERT: H 32 TYR cc_start: 0.8827 (m-80) cc_final: 0.8444 (m-80) REVERT: H 34 MET cc_start: 0.8286 (mmt) cc_final: 0.8017 (mmm) REVERT: H 60 TYR cc_start: 0.5654 (m-80) cc_final: 0.5364 (m-10) REVERT: H 89 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7270 (pp20) REVERT: H 183 TYR cc_start: 0.8434 (m-80) cc_final: 0.8083 (m-80) REVERT: J 118 VAL cc_start: 0.3265 (OUTLIER) cc_final: 0.2986 (t) outliers start: 111 outliers final: 44 residues processed: 288 average time/residue: 0.1660 time to fit residues: 84.5434 Evaluate side-chains 209 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 372 optimal weight: 40.0000 chunk 87 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 317 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 762 GLN A1054 GLN B 239 GLN B 532 ASN B1054 GLN C 895 GLN C 901 GLN C1054 GLN C1142 GLN H 112 GLN L 72 ASN F 39 GLN F 100 GLN G 72 ASN ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.154651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092966 restraints weight = 98288.337| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.74 r_work: 0.2953 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 36480 Z= 0.221 Angle : 0.678 14.320 49842 Z= 0.345 Chirality : 0.049 0.571 5775 Planarity : 0.005 0.081 6342 Dihedral : 5.169 52.953 6076 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.74 % Allowed : 21.54 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.12), residues: 4449 helix: 1.04 (0.21), residues: 660 sheet: 0.44 (0.15), residues: 1263 loop : -1.63 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 246 TYR 0.033 0.002 TYR C 369 PHE 0.026 0.002 PHE C 168 TRP 0.028 0.002 TRP C 886 HIS 0.015 0.002 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00521 (36366) covalent geometry : angle 0.65351 (49554) SS BOND : bond 0.00933 ( 54) SS BOND : angle 1.74924 ( 108) hydrogen bonds : bond 0.05991 ( 1183) hydrogen bonds : angle 5.71413 ( 3462) link_BETA1-4 : bond 0.00828 ( 15) link_BETA1-4 : angle 1.44007 ( 45) link_NAG-ASN : bond 0.01068 ( 45) link_NAG-ASN : angle 3.09573 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 150 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6699 (tt) REVERT: A 136 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7080 (p) REVERT: A 354 ASN cc_start: 0.6536 (OUTLIER) cc_final: 0.6316 (t0) REVERT: A 394 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7302 (m110) REVERT: A 645 THR cc_start: 0.9317 (t) cc_final: 0.9080 (p) REVERT: A 823 PHE cc_start: 0.8769 (t80) cc_final: 0.8467 (m-80) REVERT: B 52 GLN cc_start: 0.8276 (tp-100) cc_final: 0.8008 (tm-30) REVERT: B 136 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7210 (p) REVERT: B 197 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8591 (pp) REVERT: B 215 ASP cc_start: 0.7340 (t0) cc_final: 0.6981 (t0) REVERT: B 565 PHE cc_start: 0.7367 (m-10) cc_final: 0.7157 (m-10) REVERT: B 853 GLN cc_start: 0.5258 (mp10) cc_final: 0.4831 (mp10) REVERT: B 869 MET cc_start: 0.8930 (mmm) cc_final: 0.8718 (mtt) REVERT: B 990 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: B 1142 GLN cc_start: 0.9267 (tt0) cc_final: 0.9038 (tp40) REVERT: B 1145 LEU cc_start: 0.8265 (mt) cc_final: 0.7813 (tp) REVERT: C 136 CYS cc_start: 0.6002 (OUTLIER) cc_final: 0.5783 (p) REVERT: C 177 MET cc_start: -0.0360 (OUTLIER) cc_final: -0.4638 (ttm) REVERT: C 250 THR cc_start: 0.2063 (OUTLIER) cc_final: 0.1851 (t) REVERT: C 396 TYR cc_start: 0.8875 (m-80) cc_final: 0.8522 (m-80) REVERT: C 731 MET cc_start: 0.9144 (ptt) cc_final: 0.8893 (ptt) REVERT: C 868 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7926 (tm-30) REVERT: H 34 MET cc_start: 0.8261 (mmt) cc_final: 0.8006 (mmm) REVERT: H 57 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7788 (mp0) REVERT: H 80 TYR cc_start: 0.7791 (m-10) cc_final: 0.7363 (m-80) REVERT: H 136 LYS cc_start: 0.2697 (OUTLIER) cc_final: 0.1763 (tptt) REVERT: H 183 TYR cc_start: 0.8496 (m-80) cc_final: 0.8226 (m-80) REVERT: L 40 ARG cc_start: 0.4559 (mmp-170) cc_final: 0.3365 (mmp80) REVERT: L 95 ASP cc_start: 0.8590 (p0) cc_final: 0.7992 (p0) REVERT: L 100 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8592 (m) REVERT: J 83 MET cc_start: -0.5045 (OUTLIER) cc_final: -0.5324 (mmt) REVERT: J 118 VAL cc_start: 0.4304 (OUTLIER) cc_final: 0.4033 (t) outliers start: 145 outliers final: 65 residues processed: 281 average time/residue: 0.1795 time to fit residues: 88.4685 Evaluate side-chains 208 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 129 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 361 optimal weight: 40.0000 chunk 279 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 439 optimal weight: 50.0000 chunk 28 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 403 optimal weight: 9.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 49 HIS C 762 GLN C1083 HIS H 3 GLN H 112 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN J 39 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.153303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090769 restraints weight = 96609.435| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.67 r_work: 0.2914 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36480 Z= 0.197 Angle : 0.603 12.764 49842 Z= 0.304 Chirality : 0.047 0.490 5775 Planarity : 0.005 0.077 6342 Dihedral : 4.626 50.998 6075 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.40 % Allowed : 21.84 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.12), residues: 4449 helix: 1.27 (0.21), residues: 672 sheet: 0.65 (0.15), residues: 1206 loop : -1.60 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.022 0.002 TYR H 60 PHE 0.022 0.002 PHE L 63 TRP 0.017 0.001 TRP C 886 HIS 0.010 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00472 (36366) covalent geometry : angle 0.58051 (49554) SS BOND : bond 0.00394 ( 54) SS BOND : angle 1.53893 ( 108) hydrogen bonds : bond 0.04815 ( 1183) hydrogen bonds : angle 5.30607 ( 3462) link_BETA1-4 : bond 0.00171 ( 15) link_BETA1-4 : angle 1.07124 ( 45) link_NAG-ASN : bond 0.00498 ( 45) link_NAG-ASN : angle 2.84745 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 141 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7390 (p) REVERT: A 451 TYR cc_start: 0.4699 (t80) cc_final: 0.3960 (t80) REVERT: A 517 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8560 (mm) REVERT: A 546 LEU cc_start: 0.6360 (pt) cc_final: 0.6085 (pp) REVERT: B 136 CYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7308 (p) REVERT: B 197 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8229 (pp) REVERT: B 215 ASP cc_start: 0.7179 (t0) cc_final: 0.6766 (t0) REVERT: B 565 PHE cc_start: 0.7620 (m-10) cc_final: 0.7390 (m-10) REVERT: B 990 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: B 1142 GLN cc_start: 0.9309 (tt0) cc_final: 0.9071 (tp40) REVERT: B 1145 LEU cc_start: 0.8316 (mt) cc_final: 0.7841 (tp) REVERT: C 136 CYS cc_start: 0.5890 (OUTLIER) cc_final: 0.5531 (p) REVERT: C 177 MET cc_start: -0.0838 (OUTLIER) cc_final: -0.4575 (mtt) REVERT: C 374 PHE cc_start: 0.7527 (m-80) cc_final: 0.7036 (m-80) REVERT: C 396 TYR cc_start: 0.8860 (m-80) cc_final: 0.8500 (m-80) REVERT: C 434 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7754 (tp) REVERT: C 780 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8896 (mm-30) REVERT: C 916 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8802 (tt) REVERT: H 34 MET cc_start: 0.8227 (mmt) cc_final: 0.7974 (mmm) REVERT: H 80 TYR cc_start: 0.7877 (m-10) cc_final: 0.7642 (m-10) REVERT: H 136 LYS cc_start: 0.2623 (OUTLIER) cc_final: 0.1554 (tptt) REVERT: H 183 TYR cc_start: 0.8491 (m-80) cc_final: 0.8258 (m-80) REVERT: L 40 ARG cc_start: 0.4884 (mmp-170) cc_final: 0.3563 (mmp80) REVERT: J 83 MET cc_start: -0.4748 (OUTLIER) cc_final: -0.4988 (mmt) REVERT: J 118 VAL cc_start: 0.4301 (OUTLIER) cc_final: 0.4062 (t) REVERT: K 19 THR cc_start: 0.5524 (OUTLIER) cc_final: 0.5286 (m) outliers start: 132 outliers final: 73 residues processed: 261 average time/residue: 0.2037 time to fit residues: 93.6174 Evaluate side-chains 209 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 123 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 174 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 334 optimal weight: 50.0000 chunk 71 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 388 optimal weight: 40.0000 chunk 296 optimal weight: 1.9990 chunk 427 optimal weight: 50.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 134 GLN H 3 GLN H 39 GLN L 39 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 GLN L 199 HIS F 100 GLN ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.154545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095454 restraints weight = 94804.400| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 5.86 r_work: 0.2922 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36480 Z= 0.162 Angle : 0.571 12.788 49842 Z= 0.287 Chirality : 0.045 0.476 5775 Planarity : 0.004 0.077 6342 Dihedral : 4.392 52.173 6074 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.25 % Allowed : 21.64 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.13), residues: 4449 helix: 1.34 (0.21), residues: 691 sheet: 0.44 (0.15), residues: 1272 loop : -1.51 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 40 TYR 0.016 0.001 TYR G 37 PHE 0.017 0.001 PHE A1121 TRP 0.013 0.001 TRP A 436 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00389 (36366) covalent geometry : angle 0.55037 (49554) SS BOND : bond 0.00323 ( 54) SS BOND : angle 1.45408 ( 108) hydrogen bonds : bond 0.04694 ( 1183) hydrogen bonds : angle 5.12501 ( 3462) link_BETA1-4 : bond 0.00218 ( 15) link_BETA1-4 : angle 1.02684 ( 45) link_NAG-ASN : bond 0.00465 ( 45) link_NAG-ASN : angle 2.65980 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 123 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7066 (p) REVERT: A 242 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7701 (mp) REVERT: A 546 LEU cc_start: 0.6426 (pt) cc_final: 0.6106 (pp) REVERT: A 583 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8216 (pm20) REVERT: B 197 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8582 (pp) REVERT: B 215 ASP cc_start: 0.7150 (t0) cc_final: 0.6772 (t0) REVERT: B 529 LYS cc_start: 0.8476 (mmtm) cc_final: 0.7854 (tppt) REVERT: B 565 PHE cc_start: 0.7719 (m-10) cc_final: 0.7376 (m-10) REVERT: B 913 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9048 (pt0) REVERT: B 990 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: B 1142 GLN cc_start: 0.9301 (tt0) cc_final: 0.9088 (tp40) REVERT: B 1145 LEU cc_start: 0.8502 (mt) cc_final: 0.8180 (tp) REVERT: C 136 CYS cc_start: 0.5287 (OUTLIER) cc_final: 0.4988 (p) REVERT: C 177 MET cc_start: -0.0258 (OUTLIER) cc_final: -0.4066 (mtt) REVERT: C 374 PHE cc_start: 0.7263 (m-80) cc_final: 0.7032 (m-80) REVERT: C 916 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8792 (tt) REVERT: H 34 MET cc_start: 0.8175 (mmt) cc_final: 0.7937 (mmm) REVERT: H 80 TYR cc_start: 0.7683 (m-10) cc_final: 0.7382 (m-80) REVERT: H 136 LYS cc_start: -0.0778 (OUTLIER) cc_final: -0.3111 (tptt) REVERT: H 183 TYR cc_start: 0.8451 (m-80) cc_final: 0.8154 (m-80) REVERT: L 40 ARG cc_start: 0.4878 (mmp-170) cc_final: 0.3635 (mmp80) REVERT: J 13 GLN cc_start: 0.1047 (OUTLIER) cc_final: 0.0592 (pm20) REVERT: J 118 VAL cc_start: 0.2713 (OUTLIER) cc_final: 0.2384 (t) REVERT: K 3 MET cc_start: 0.6303 (tpt) cc_final: 0.6005 (tpt) outliers start: 126 outliers final: 77 residues processed: 241 average time/residue: 0.2177 time to fit residues: 91.6956 Evaluate side-chains 208 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 119 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 174 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 7 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 235 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 307 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 376 optimal weight: 20.0000 chunk 393 optimal weight: 30.0000 chunk 324 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN H 3 GLN L 72 ASN F 100 GLN ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.153756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091289 restraints weight = 96881.743| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.40 r_work: 0.2937 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36480 Z= 0.166 Angle : 0.564 11.637 49842 Z= 0.284 Chirality : 0.045 0.473 5775 Planarity : 0.004 0.076 6342 Dihedral : 4.276 54.275 6072 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 3.07 % Allowed : 22.00 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.13), residues: 4449 helix: 1.44 (0.21), residues: 691 sheet: 0.47 (0.15), residues: 1279 loop : -1.50 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.031 0.001 TYR H 59 PHE 0.018 0.001 PHE C 168 TRP 0.010 0.001 TRP C 886 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00400 (36366) covalent geometry : angle 0.54448 (49554) SS BOND : bond 0.00308 ( 54) SS BOND : angle 1.46243 ( 108) hydrogen bonds : bond 0.04623 ( 1183) hydrogen bonds : angle 5.02678 ( 3462) link_BETA1-4 : bond 0.00221 ( 15) link_BETA1-4 : angle 1.03909 ( 45) link_NAG-ASN : bond 0.00431 ( 45) link_NAG-ASN : angle 2.59431 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 125 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7038 (p) REVERT: A 546 LEU cc_start: 0.6620 (pt) cc_final: 0.6283 (pp) REVERT: A 583 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: B 197 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 215 ASP cc_start: 0.7135 (t0) cc_final: 0.6337 (t0) REVERT: B 293 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8920 (tp) REVERT: B 529 LYS cc_start: 0.8712 (mmtm) cc_final: 0.7960 (tppt) REVERT: B 565 PHE cc_start: 0.7709 (m-10) cc_final: 0.7378 (m-10) REVERT: B 814 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8726 (mptt) REVERT: B 990 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8393 (tm-30) REVERT: B 1145 LEU cc_start: 0.8539 (mt) cc_final: 0.8281 (tp) REVERT: C 136 CYS cc_start: 0.5332 (OUTLIER) cc_final: 0.4993 (p) REVERT: C 177 MET cc_start: 0.0016 (OUTLIER) cc_final: -0.3766 (mtt) REVERT: C 916 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8811 (tt) REVERT: C 1144 GLU cc_start: 0.8617 (tp30) cc_final: 0.7813 (mp0) REVERT: H 34 MET cc_start: 0.8171 (mmt) cc_final: 0.7869 (mmt) REVERT: H 80 TYR cc_start: 0.7736 (m-10) cc_final: 0.7429 (m-80) REVERT: H 136 LYS cc_start: -0.0702 (OUTLIER) cc_final: -0.2865 (tptt) REVERT: H 183 TYR cc_start: 0.8489 (m-80) cc_final: 0.8212 (m-80) REVERT: L 40 ARG cc_start: 0.4957 (mmp-170) cc_final: 0.3596 (mmp80) REVERT: L 64 SER cc_start: -0.0750 (OUTLIER) cc_final: -0.1204 (t) REVERT: F 112 GLN cc_start: 0.8168 (mp10) cc_final: 0.7918 (pm20) REVERT: G 40 ARG cc_start: 0.5490 (mmp80) cc_final: 0.5274 (mmt180) REVERT: J 13 GLN cc_start: 0.0710 (OUTLIER) cc_final: 0.0364 (pm20) REVERT: J 118 VAL cc_start: 0.3061 (OUTLIER) cc_final: 0.2752 (t) REVERT: K 19 THR cc_start: 0.5480 (OUTLIER) cc_final: 0.5240 (m) outliers start: 119 outliers final: 91 residues processed: 238 average time/residue: 0.2031 time to fit residues: 84.2185 Evaluate side-chains 224 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 119 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 174 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 73 optimal weight: 3.9990 chunk 164 optimal weight: 0.0000 chunk 52 optimal weight: 1.9990 chunk 387 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 152 optimal weight: 0.0020 chunk 365 optimal weight: 2.9990 chunk 433 optimal weight: 50.0000 chunk 86 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.155515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.092875 restraints weight = 98143.393| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 4.14 r_work: 0.2956 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36480 Z= 0.138 Angle : 0.538 10.947 49842 Z= 0.271 Chirality : 0.044 0.448 5775 Planarity : 0.004 0.077 6342 Dihedral : 4.111 55.345 6068 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.77 % Favored : 95.21 % Rotamer: Outliers : 3.22 % Allowed : 22.05 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.13), residues: 4449 helix: 1.58 (0.21), residues: 691 sheet: 0.43 (0.15), residues: 1257 loop : -1.41 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.013 0.001 TYR C 265 PHE 0.022 0.001 PHE B 855 TRP 0.010 0.001 TRP C 436 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00331 (36366) covalent geometry : angle 0.51948 (49554) SS BOND : bond 0.00272 ( 54) SS BOND : angle 1.31401 ( 108) hydrogen bonds : bond 0.04324 ( 1183) hydrogen bonds : angle 4.90786 ( 3462) link_BETA1-4 : bond 0.00271 ( 15) link_BETA1-4 : angle 0.98742 ( 45) link_NAG-ASN : bond 0.00415 ( 45) link_NAG-ASN : angle 2.48131 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 120 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8334 (mmm160) REVERT: A 136 CYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6984 (p) REVERT: A 242 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7568 (mp) REVERT: A 546 LEU cc_start: 0.6841 (pt) cc_final: 0.6251 (pp) REVERT: A 583 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: B 197 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8582 (pp) REVERT: B 529 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8080 (tppt) REVERT: B 565 PHE cc_start: 0.7712 (m-10) cc_final: 0.7412 (m-10) REVERT: B 814 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8732 (mptt) REVERT: B 990 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: B 1145 LEU cc_start: 0.8393 (mt) cc_final: 0.8185 (tp) REVERT: C 136 CYS cc_start: 0.5344 (OUTLIER) cc_final: 0.4997 (p) REVERT: C 177 MET cc_start: 0.0158 (OUTLIER) cc_final: -0.3672 (mtt) REVERT: C 396 TYR cc_start: 0.8299 (m-80) cc_final: 0.7900 (m-80) REVERT: C 724 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9352 (m) REVERT: C 916 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8765 (tt) REVERT: C 1144 GLU cc_start: 0.8652 (tp30) cc_final: 0.8288 (tp30) REVERT: H 34 MET cc_start: 0.8208 (mmt) cc_final: 0.7899 (mmt) REVERT: H 80 TYR cc_start: 0.7788 (m-10) cc_final: 0.7510 (m-80) REVERT: H 136 LYS cc_start: -0.0743 (OUTLIER) cc_final: -0.2943 (tptt) REVERT: H 183 TYR cc_start: 0.8540 (m-80) cc_final: 0.8249 (m-80) REVERT: L 64 SER cc_start: -0.0717 (OUTLIER) cc_final: -0.1186 (t) REVERT: J 13 GLN cc_start: 0.0701 (OUTLIER) cc_final: 0.0304 (pm20) REVERT: J 118 VAL cc_start: 0.2832 (OUTLIER) cc_final: 0.2451 (t) REVERT: K 19 THR cc_start: 0.5434 (OUTLIER) cc_final: 0.5124 (m) outliers start: 125 outliers final: 90 residues processed: 236 average time/residue: 0.1989 time to fit residues: 82.4179 Evaluate side-chains 223 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 117 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 TYR Chi-restraints excluded: chain K residue 174 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 329 optimal weight: 50.0000 chunk 411 optimal weight: 50.0000 chunk 229 optimal weight: 7.9990 chunk 391 optimal weight: 50.0000 chunk 149 optimal weight: 40.0000 chunk 373 optimal weight: 20.0000 chunk 141 optimal weight: 40.0000 chunk 23 optimal weight: 6.9990 chunk 218 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 14 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 334 ASN B 895 GLN B1106 GLN C 544 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.152618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089677 restraints weight = 97347.882| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.03 r_work: 0.2807 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.121 36480 Z= 0.394 Angle : 0.777 12.237 49842 Z= 0.395 Chirality : 0.053 0.671 5775 Planarity : 0.005 0.075 6342 Dihedral : 5.143 51.797 6068 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.43 % Favored : 93.55 % Rotamer: Outliers : 3.45 % Allowed : 21.74 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.12), residues: 4449 helix: 0.63 (0.20), residues: 684 sheet: 0.23 (0.14), residues: 1293 loop : -1.60 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.022 0.002 TYR B 756 PHE 0.042 0.003 PHE A1121 TRP 0.016 0.002 TRP C 886 HIS 0.015 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00962 (36366) covalent geometry : angle 0.75104 (49554) SS BOND : bond 0.00546 ( 54) SS BOND : angle 2.17473 ( 108) hydrogen bonds : bond 0.07085 ( 1183) hydrogen bonds : angle 5.53994 ( 3462) link_BETA1-4 : bond 0.00283 ( 15) link_BETA1-4 : angle 1.37573 ( 45) link_NAG-ASN : bond 0.00694 ( 45) link_NAG-ASN : angle 3.35884 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 119 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7370 (p) REVERT: A 583 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: A 645 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9097 (p) REVERT: A 856 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8374 (t0) REVERT: B 177 MET cc_start: 0.2776 (mpp) cc_final: -0.1773 (ptt) REVERT: B 197 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8454 (pp) REVERT: B 902 MET cc_start: 0.9287 (tpt) cc_final: 0.9066 (mmm) REVERT: B 1145 LEU cc_start: 0.8598 (mt) cc_final: 0.8292 (tp) REVERT: C 136 CYS cc_start: 0.5426 (OUTLIER) cc_final: 0.4943 (p) REVERT: C 177 MET cc_start: -0.0123 (OUTLIER) cc_final: -0.4109 (mtt) REVERT: C 294 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: C 916 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8825 (tt) REVERT: C 1144 GLU cc_start: 0.8928 (tp30) cc_final: 0.8652 (tp30) REVERT: H 34 MET cc_start: 0.8292 (mmt) cc_final: 0.7950 (mmt) REVERT: H 136 LYS cc_start: 0.0691 (OUTLIER) cc_final: -0.1060 (tptt) REVERT: H 183 TYR cc_start: 0.8576 (m-80) cc_final: 0.8306 (m-80) REVERT: L 64 SER cc_start: -0.0504 (OUTLIER) cc_final: -0.0955 (t) REVERT: J 13 GLN cc_start: 0.1294 (OUTLIER) cc_final: 0.0859 (pm20) REVERT: J 118 VAL cc_start: 0.4005 (OUTLIER) cc_final: 0.3659 (t) REVERT: K 19 THR cc_start: 0.5649 (OUTLIER) cc_final: 0.5424 (m) REVERT: K 125 SER cc_start: 0.4114 (m) cc_final: 0.3898 (p) outliers start: 134 outliers final: 96 residues processed: 245 average time/residue: 0.1994 time to fit residues: 86.2011 Evaluate side-chains 224 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 114 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 66 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 388 optimal weight: 0.9990 chunk 347 optimal weight: 50.0000 chunk 84 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 422 optimal weight: 40.0000 chunk 32 optimal weight: 7.9990 chunk 312 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 856 ASN B 14 GLN L 38 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087085 restraints weight = 95493.203| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 4.38 r_work: 0.2896 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 36480 Z= 0.109 Angle : 0.567 11.670 49842 Z= 0.285 Chirality : 0.044 0.449 5775 Planarity : 0.004 0.076 6342 Dihedral : 4.519 55.748 6068 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 2.09 % Allowed : 23.00 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.13), residues: 4449 helix: 1.45 (0.21), residues: 680 sheet: 0.31 (0.15), residues: 1266 loop : -1.44 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 78 TYR 0.016 0.001 TYR C 265 PHE 0.025 0.001 PHE B 855 TRP 0.014 0.001 TRP C 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00245 (36366) covalent geometry : angle 0.54764 (49554) SS BOND : bond 0.00250 ( 54) SS BOND : angle 1.35995 ( 108) hydrogen bonds : bond 0.04478 ( 1183) hydrogen bonds : angle 4.98934 ( 3462) link_BETA1-4 : bond 0.00430 ( 15) link_BETA1-4 : angle 0.93961 ( 45) link_NAG-ASN : bond 0.00513 ( 45) link_NAG-ASN : angle 2.63274 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 118 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7300 (p) REVERT: A 242 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7455 (mp) REVERT: A 583 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: A 856 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8384 (t0) REVERT: A 934 ILE cc_start: 0.8441 (tp) cc_final: 0.8065 (mm) REVERT: B 177 MET cc_start: 0.2805 (mpp) cc_final: -0.1883 (ptt) REVERT: B 197 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8456 (pp) REVERT: B 529 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8084 (tppt) REVERT: B 1029 MET cc_start: 0.9114 (tpp) cc_final: 0.8808 (tpp) REVERT: C 136 CYS cc_start: 0.5474 (OUTLIER) cc_final: 0.5088 (p) REVERT: C 177 MET cc_start: -0.0483 (mtt) cc_final: -0.4209 (mtt) REVERT: C 396 TYR cc_start: 0.8455 (m-80) cc_final: 0.8094 (m-80) REVERT: C 916 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8710 (tt) REVERT: C 1144 GLU cc_start: 0.8951 (tp30) cc_final: 0.8570 (tp30) REVERT: H 34 MET cc_start: 0.8230 (mmt) cc_final: 0.7951 (mmt) REVERT: H 136 LYS cc_start: 0.1342 (OUTLIER) cc_final: -0.0229 (tptt) REVERT: H 183 TYR cc_start: 0.8569 (m-80) cc_final: 0.8316 (m-80) REVERT: L 64 SER cc_start: -0.0505 (OUTLIER) cc_final: -0.0951 (t) REVERT: K 19 THR cc_start: 0.5650 (OUTLIER) cc_final: 0.5424 (m) outliers start: 81 outliers final: 63 residues processed: 193 average time/residue: 0.2003 time to fit residues: 68.4689 Evaluate side-chains 187 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 114 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 292 optimal weight: 0.6980 chunk 328 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 371 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 293 optimal weight: 0.8980 chunk 290 optimal weight: 0.8980 chunk 307 optimal weight: 0.7980 chunk 398 optimal weight: 30.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN ** G 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS K 98 ASN ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.152843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090211 restraints weight = 94627.338| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 4.26 r_work: 0.2941 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36480 Z= 0.106 Angle : 0.544 11.615 49842 Z= 0.272 Chirality : 0.044 0.439 5775 Planarity : 0.004 0.077 6342 Dihedral : 4.230 57.623 6068 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.79 % Favored : 95.19 % Rotamer: Outliers : 1.98 % Allowed : 22.98 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.13), residues: 4449 helix: 1.73 (0.21), residues: 681 sheet: 0.36 (0.15), residues: 1263 loop : -1.38 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 78 TYR 0.020 0.001 TYR F 109 PHE 0.024 0.001 PHE C 374 TRP 0.018 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00242 (36366) covalent geometry : angle 0.52623 (49554) SS BOND : bond 0.00253 ( 54) SS BOND : angle 1.29536 ( 108) hydrogen bonds : bond 0.04041 ( 1183) hydrogen bonds : angle 4.81204 ( 3462) link_BETA1-4 : bond 0.00317 ( 15) link_BETA1-4 : angle 0.98418 ( 45) link_NAG-ASN : bond 0.00448 ( 45) link_NAG-ASN : angle 2.43445 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 119 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7426 (p) REVERT: A 583 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: B 177 MET cc_start: 0.2500 (mpp) cc_final: -0.2068 (ptt) REVERT: B 197 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8308 (pp) REVERT: B 529 LYS cc_start: 0.8936 (mmtm) cc_final: 0.8123 (tppt) REVERT: B 565 PHE cc_start: 0.7760 (m-10) cc_final: 0.7557 (m-10) REVERT: C 177 MET cc_start: -0.0806 (mtt) cc_final: -0.4260 (mtt) REVERT: C 396 TYR cc_start: 0.8270 (m-80) cc_final: 0.7813 (m-80) REVERT: C 724 THR cc_start: 0.9588 (OUTLIER) cc_final: 0.9375 (m) REVERT: C 1144 GLU cc_start: 0.8947 (tp30) cc_final: 0.8600 (tp30) REVERT: H 34 MET cc_start: 0.8323 (mmt) cc_final: 0.8025 (mmt) REVERT: H 80 TYR cc_start: 0.7939 (m-10) cc_final: 0.7660 (m-10) REVERT: H 136 LYS cc_start: -0.0305 (OUTLIER) cc_final: -0.2412 (tptt) REVERT: H 183 TYR cc_start: 0.8616 (m-80) cc_final: 0.8339 (m-80) REVERT: L 64 SER cc_start: -0.0589 (OUTLIER) cc_final: -0.1083 (t) REVERT: K 19 THR cc_start: 0.5499 (OUTLIER) cc_final: 0.5254 (m) outliers start: 77 outliers final: 64 residues processed: 192 average time/residue: 0.1765 time to fit residues: 60.8174 Evaluate side-chains 185 residues out of total 3909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 114 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 212 optimal weight: 30.0000 chunk 200 optimal weight: 3.9990 chunk 410 optimal weight: 30.0000 chunk 285 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 424 optimal weight: 50.0000 chunk 177 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 389 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS K 178 GLN ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.148749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084890 restraints weight = 95757.837| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 4.29 r_work: 0.2892 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 36480 Z= 0.215 Angle : 0.616 12.152 49842 Z= 0.310 Chirality : 0.046 0.513 5775 Planarity : 0.005 0.074 6342 Dihedral : 4.474 55.700 6068 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.83 % Rotamer: Outliers : 2.19 % Allowed : 22.80 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.13), residues: 4449 helix: 1.42 (0.21), residues: 687 sheet: 0.29 (0.15), residues: 1289 loop : -1.39 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 246 TYR 0.015 0.001 TYR C 279 PHE 0.026 0.002 PHE A1121 TRP 0.047 0.001 TRP C 152 HIS 0.010 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00525 (36366) covalent geometry : angle 0.59626 (49554) SS BOND : bond 0.00309 ( 54) SS BOND : angle 1.62662 ( 108) hydrogen bonds : bond 0.05206 ( 1183) hydrogen bonds : angle 5.01267 ( 3462) link_BETA1-4 : bond 0.00164 ( 15) link_BETA1-4 : angle 1.04140 ( 45) link_NAG-ASN : bond 0.00463 ( 45) link_NAG-ASN : angle 2.66095 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14352.79 seconds wall clock time: 244 minutes 37.26 seconds (14677.26 seconds total)