Starting phenix.real_space_refine on Mon Aug 25 08:40:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gxe_51659/08_2025/9gxe_51659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gxe_51659/08_2025/9gxe_51659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gxe_51659/08_2025/9gxe_51659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gxe_51659/08_2025/9gxe_51659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gxe_51659/08_2025/9gxe_51659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gxe_51659/08_2025/9gxe_51659.map" } resolution = 2.3 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 16806 2.51 5 N 4348 2.21 5 O 5231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s 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: 26514 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8542 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 57, 'TRANS': 1034} Chain breaks: 5 Chain: "B" Number of atoms: 8491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8491 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1028} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 8406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8406 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 56, 'TRANS': 1018} Chain breaks: 8 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 54 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'4J5:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'0JY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 54 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'4J5:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'0JY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 54 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'4J5:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'0JY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AA" 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: "AB" 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: "AC" 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: "BA" 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: "BB" 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: "BC" 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: "CA" 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: "CB" 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: "CC" 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: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 118 Unusual residues: {'NAG': 7, 'STE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 132 Unusual residues: {'NAG': 8, 'STE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'NAG': 6, 'STE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'KZ0': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 6 Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'KZ0': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 6 Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'KZ0': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 6.82, per 1000 atoms: 0.26 Number of scatterers: 26514 At special positions: 0 Unit cell: (137.235, 145.022, 175.194, 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 129 16.00 O 5231 8.00 N 4348 7.00 C 16806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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=2.05 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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=2.04 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 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " 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 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 additional links: simple=3, symmetry=0 Simple link: pdb=" C LEU D 9 " - pdb=" N 0JY D 10 " Simple link: pdb=" C LEU E 9 " - pdb=" N 0JY E 10 " Simple link: pdb=" C LEU F 9 " - pdb=" N 0JY F 10 " Number of custom bonds: simple=15, symmetry=0 Links applied BETA1-4 " NAGAA 1 " - " NAGAA 2 " " NAGAB 1 " - " NAGAB 2 " " NAGAC 1 " - " NAGAC 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBB 1 " - " NAGBB 2 " " NAGBC 1 " - " NAGBC 2 " " NAGCA 1 " - " NAGCA 2 " " NAGCB 1 " - " NAGCB 2 " " NAGCC 1 " - " NAGCC 2 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A 17 " " NAG A1203 " - " ASN A 122 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 343 " " NAG A1206 " - " ASN A 616 " " NAG A1207 " - " ASN A 801 " " NAG B1201 " - " ASN B 709 " " NAG B1202 " - " ASN B1134 " " NAG B1203 " - " ASN B 17 " " NAG B1204 " - " ASN B1074 " " NAG B1205 " - " ASN B 343 " " NAG B1206 " - " ASN B 122 " " NAG B1207 " - " ASN B 234 " " NAG B1208 " - " ASN B 616 " " NAG C1201 " - " ASN C 709 " " NAG C1202 " - " ASN C 17 " " NAG C1203 " - " ASN C 122 " " NAG C1204 " - " ASN C1074 " " NAG C1205 " - " ASN C1134 " " NAG C1206 " - " ASN C 234 " " NAGAA 1 " - " ASN A1098 " " NAGAB 1 " - " ASN A1134 " " NAGAC 1 " - " ASN A 717 " " NAGBA 1 " - " ASN B 801 " " NAGBB 1 " - " ASN B1098 " " NAGBC 1 " - " ASN B 717 " " NAGCA 1 " - " ASN C 801 " " NAGCB 1 " - " ASN C 717 " " NAGCC 1 " - " ASN C1098 " Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 7 " pdb=" CB DAL E 7 " pdb=" CB DAL F 7 " Number of C-beta restraints generated: 6158 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 50 sheets defined 23.3% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.722A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.345A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.391A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.503A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.663A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.528A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.097A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.742A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.546A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.440A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.717A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.592A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.697A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.099A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.558A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.922A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.599A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.357A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.723A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.043A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 982 Processing helix chain 'C' and resid 985 through 1032 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.009A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.009A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.600A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.700A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 167 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.668A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.709A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.825A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 167 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.551A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.081A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.569A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) 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 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.233A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.891A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.597A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.597A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.422A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 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 31 removed outlier: 4.024A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.024A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.686A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.818A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 152 through 163 removed outlier: 6.533A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 13.144A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.390A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.769A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.320A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) 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 Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.151A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.191A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (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 728 removed outlier: 6.474A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.474A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.400A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) 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 31 removed outlier: 4.015A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 78 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.015A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.819A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.246A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.836A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 391 through 392 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 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.264A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.477A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.477A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.331A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 1103 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.12 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4404 1.32 - 1.46: 9809 1.46 - 1.60: 12586 1.60 - 1.73: 0 1.73 - 1.87: 159 Bond restraints: 26958 Sorted by residual: bond pdb=" CE 4J5 D 6 " pdb=" NH2 4J5 D 6 " ideal model delta sigma weight residual 1.323 1.470 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" CE 4J5 F 6 " pdb=" NH2 4J5 F 6 " ideal model delta sigma weight residual 1.323 1.469 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" CE 4J5 E 6 " pdb=" NH2 4J5 E 6 " ideal model delta sigma weight residual 1.323 1.469 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C ACE F 0 " pdb=" N CYS F 0A" ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C ACE E 0 " pdb=" N CYS E 0A" ideal model delta sigma weight residual 1.329 1.447 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 26953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 36369 3.21 - 6.42: 261 6.42 - 9.64: 22 9.64 - 12.85: 5 12.85 - 16.06: 2 Bond angle restraints: 36659 Sorted by residual: angle pdb=" CB MET A 153 " pdb=" CG MET A 153 " pdb=" SD MET A 153 " ideal model delta sigma weight residual 112.70 128.76 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 114.40 125.42 -11.02 2.30e+00 1.89e-01 2.29e+01 angle pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 114.40 125.31 -10.91 2.30e+00 1.89e-01 2.25e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.48 -5.78 1.22e+00 6.72e-01 2.24e+01 angle pdb=" CA GLY B 416 " pdb=" C GLY B 416 " pdb=" N LYS B 417 " ideal model delta sigma weight residual 114.23 118.37 -4.14 8.80e-01 1.29e+00 2.22e+01 ... (remaining 36654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 14504 18.07 - 36.15: 1520 36.15 - 54.22: 438 54.22 - 72.30: 92 72.30 - 90.37: 40 Dihedral angle restraints: 16594 sinusoidal: 7023 harmonic: 9571 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 -176.63 -90.37 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual 93.00 -177.02 -89.98 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 -178.15 -88.85 1 1.00e+01 1.00e-02 9.41e+01 ... (remaining 16591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3081 0.050 - 0.100: 874 0.100 - 0.151: 268 0.151 - 0.201: 23 0.201 - 0.251: 6 Chirality restraints: 4252 Sorted by residual: chirality pdb=" CB ILE A 794 " pdb=" CA ILE A 794 " pdb=" CG1 ILE A 794 " pdb=" CG2 ILE A 794 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU C 18 " pdb=" CB LEU C 18 " pdb=" CD1 LEU C 18 " pdb=" CD2 LEU C 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 794 " pdb=" CA ILE B 794 " pdb=" CG1 ILE B 794 " pdb=" CG2 ILE B 794 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 4249 not shown) Planarity restraints: 4719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.057 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO A 986 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C1142 " 0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO C1143 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C1143 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C1143 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1142 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A1143 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A1143 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1143 " 0.045 5.00e-02 4.00e+02 ... (remaining 4716 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6241 2.79 - 3.32: 21465 3.32 - 3.85: 45761 3.85 - 4.37: 54252 4.37 - 4.90: 92889 Nonbonded interactions: 220608 Sorted by model distance: nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.317 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.321 3.040 nonbonded pdb=" O SER C 31 " pdb=" OG SER C 31 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.332 3.040 ... (remaining 220603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 69 or resid 77 through 144 or resid 151 through \ 244 or resid 246 through 247 or resid 254 through 1206)) selection = (chain 'B' and (resid 14 through 69 or resid 77 through 144 or resid 151 through \ 244 or resid 246 through 247 or resid 254 through 1206)) selection = (chain 'C' and resid 14 through 1206) } ncs_group { reference = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'CA' selection = chain 'CB' selection = chain 'CC' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.300 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 27059 Z= 0.366 Angle : 0.785 18.990 36873 Z= 0.404 Chirality : 0.052 0.251 4252 Planarity : 0.007 0.085 4686 Dihedral : 16.601 89.711 10295 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.13 % Allowed : 18.34 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % 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: -0.99 (0.13), residues: 3223 helix: -0.04 (0.18), residues: 688 sheet: 0.27 (0.18), residues: 740 loop : -1.33 (0.13), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 357 TYR 0.026 0.002 TYR A1067 PHE 0.017 0.002 PHE B 238 TRP 0.012 0.002 TRP B 64 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00544 (26958) covalent geometry : angle 0.76100 (36659) SS BOND : bond 0.00600 ( 44) SS BOND : angle 1.83747 ( 88) hydrogen bonds : bond 0.11188 ( 1048) hydrogen bonds : angle 7.42551 ( 3024) Misc. bond : bond 0.11286 ( 15) link_BETA1-4 : bond 0.00653 ( 9) link_BETA1-4 : angle 1.50901 ( 27) link_NAG-ASN : bond 0.00615 ( 30) link_NAG-ASN : angle 3.54395 ( 90) link_TRANS : bond 0.00214 ( 3) link_TRANS : angle 0.34416 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 90 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 988 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7774 (pm20) REVERT: B 988 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7857 (mt-10) outliers start: 90 outliers final: 82 residues processed: 177 average time/residue: 0.5196 time to fit residues: 112.9829 Evaluate side-chains 168 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 86 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076372 restraints weight = 45303.069| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.21 r_work: 0.3002 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27059 Z= 0.213 Angle : 0.597 15.077 36873 Z= 0.307 Chirality : 0.046 0.186 4252 Planarity : 0.005 0.077 4686 Dihedral : 8.067 59.425 4524 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.06 % Allowed : 17.19 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % 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: -0.39 (0.14), residues: 3223 helix: 1.19 (0.20), residues: 710 sheet: 0.29 (0.18), residues: 754 loop : -1.14 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1000 TYR 0.024 0.002 TYR B1067 PHE 0.018 0.001 PHE C 898 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00503 (26958) covalent geometry : angle 0.57205 (36659) SS BOND : bond 0.00418 ( 44) SS BOND : angle 1.72319 ( 88) hydrogen bonds : bond 0.05144 ( 1048) hydrogen bonds : angle 6.11299 ( 3024) Misc. bond : bond 0.00173 ( 15) link_BETA1-4 : bond 0.00175 ( 9) link_BETA1-4 : angle 1.42706 ( 27) link_NAG-ASN : bond 0.00472 ( 30) link_NAG-ASN : angle 3.00174 ( 90) link_TRANS : bond 0.00211 ( 3) link_TRANS : angle 0.27635 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 91 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6233 (mmm) cc_final: 0.5939 (mmt) REVERT: A 270 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7081 (mt) REVERT: C 177 MET cc_start: 0.6490 (ttt) cc_final: 0.5642 (ttt) outliers start: 88 outliers final: 53 residues processed: 175 average time/residue: 0.5639 time to fit residues: 119.2925 Evaluate side-chains 142 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 937 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 186 optimal weight: 0.3980 chunk 277 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076593 restraints weight = 45331.337| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.21 r_work: 0.3006 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27059 Z= 0.176 Angle : 0.567 14.157 36873 Z= 0.290 Chirality : 0.045 0.181 4252 Planarity : 0.004 0.070 4686 Dihedral : 7.189 59.781 4470 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.89 % Allowed : 17.19 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % 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: -0.17 (0.14), residues: 3223 helix: 1.64 (0.20), residues: 697 sheet: 0.35 (0.18), residues: 743 loop : -1.06 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.022 0.001 TYR B1067 PHE 0.016 0.001 PHE C 898 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00413 (26958) covalent geometry : angle 0.54402 (36659) SS BOND : bond 0.00427 ( 44) SS BOND : angle 1.56824 ( 88) hydrogen bonds : bond 0.04743 ( 1048) hydrogen bonds : angle 5.90440 ( 3024) Misc. bond : bond 0.00033 ( 15) link_BETA1-4 : bond 0.00188 ( 9) link_BETA1-4 : angle 1.28939 ( 27) link_NAG-ASN : bond 0.00460 ( 30) link_NAG-ASN : angle 2.85193 ( 90) link_TRANS : bond 0.00243 ( 3) link_TRANS : angle 0.13951 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 96 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 270 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7110 (mt) REVERT: A 523 THR cc_start: 0.8198 (p) cc_final: 0.7897 (p) REVERT: B 661 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: B 755 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: B 988 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8273 (mt-10) REVERT: C 177 MET cc_start: 0.6502 (ttt) cc_final: 0.5855 (ttt) REVERT: C 469 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7881 (p) outliers start: 83 outliers final: 51 residues processed: 172 average time/residue: 0.5801 time to fit residues: 120.1910 Evaluate side-chains 146 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 91 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 314 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 235 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 chunk 252 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.106418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.075354 restraints weight = 45183.496| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.20 r_work: 0.2981 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27059 Z= 0.242 Angle : 0.616 15.052 36873 Z= 0.314 Chirality : 0.047 0.192 4252 Planarity : 0.004 0.070 4686 Dihedral : 6.961 59.295 4456 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.92 % Allowed : 17.33 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % 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: -0.20 (0.14), residues: 3223 helix: 1.65 (0.20), residues: 698 sheet: 0.31 (0.18), residues: 746 loop : -1.09 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 21 TYR 0.022 0.002 TYR B1067 PHE 0.018 0.002 PHE C 898 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00581 (26958) covalent geometry : angle 0.59027 (36659) SS BOND : bond 0.00453 ( 44) SS BOND : angle 1.93299 ( 88) hydrogen bonds : bond 0.05214 ( 1048) hydrogen bonds : angle 5.96670 ( 3024) Misc. bond : bond 0.00039 ( 15) link_BETA1-4 : bond 0.00156 ( 9) link_BETA1-4 : angle 1.49928 ( 27) link_NAG-ASN : bond 0.00514 ( 30) link_NAG-ASN : angle 3.05259 ( 90) link_TRANS : bond 0.00319 ( 3) link_TRANS : angle 0.11514 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 93 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5883 (mmm) cc_final: 0.5630 (mmt) REVERT: A 270 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7241 (mt) REVERT: A 523 THR cc_start: 0.8214 (p) cc_final: 0.7923 (p) REVERT: B 661 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: B 755 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6868 (mp10) REVERT: B 988 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 177 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6023 (ttt) REVERT: C 469 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7826 (p) REVERT: C 780 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8704 (mt-10) REVERT: C 985 ASP cc_start: 0.7495 (p0) cc_final: 0.7205 (p0) REVERT: C 988 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: C 1142 GLN cc_start: 0.8754 (pp30) cc_final: 0.8455 (pp30) outliers start: 84 outliers final: 56 residues processed: 170 average time/residue: 0.4956 time to fit residues: 101.9168 Evaluate side-chains 155 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 92 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 188 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 260 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076421 restraints weight = 44913.477| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.20 r_work: 0.3004 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27059 Z= 0.167 Angle : 0.564 14.236 36873 Z= 0.288 Chirality : 0.044 0.193 4252 Planarity : 0.004 0.068 4686 Dihedral : 6.653 58.898 4455 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.82 % Allowed : 17.54 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: -0.10 (0.14), residues: 3223 helix: 1.79 (0.20), residues: 698 sheet: 0.34 (0.19), residues: 740 loop : -1.03 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE C 898 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00392 (26958) covalent geometry : angle 0.53954 (36659) SS BOND : bond 0.00437 ( 44) SS BOND : angle 1.73379 ( 88) hydrogen bonds : bond 0.04640 ( 1048) hydrogen bonds : angle 5.80888 ( 3024) Misc. bond : bond 0.00023 ( 15) link_BETA1-4 : bond 0.00180 ( 9) link_BETA1-4 : angle 1.29198 ( 27) link_NAG-ASN : bond 0.00457 ( 30) link_NAG-ASN : angle 2.86812 ( 90) link_TRANS : bond 0.00216 ( 3) link_TRANS : angle 0.14031 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 94 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 270 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7132 (mt) REVERT: A 523 THR cc_start: 0.8159 (p) cc_final: 0.7855 (p) REVERT: B 661 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: B 755 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: C 177 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6020 (ttt) REVERT: C 469 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7848 (p) REVERT: C 528 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7843 (mttp) REVERT: C 985 ASP cc_start: 0.7460 (p0) cc_final: 0.7190 (p0) REVERT: C 988 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: C 1142 GLN cc_start: 0.8752 (pp30) cc_final: 0.8427 (pp30) outliers start: 81 outliers final: 58 residues processed: 166 average time/residue: 0.6020 time to fit residues: 121.0628 Evaluate side-chains 157 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 92 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 269 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 320 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 110 optimal weight: 0.0870 chunk 291 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1054 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.108528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077804 restraints weight = 44912.104| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.20 r_work: 0.3030 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27059 Z= 0.124 Angle : 0.526 13.078 36873 Z= 0.269 Chirality : 0.043 0.194 4252 Planarity : 0.004 0.067 4686 Dihedral : 6.226 59.468 4449 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.37 % Allowed : 17.95 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: 0.02 (0.14), residues: 3223 helix: 1.94 (0.20), residues: 698 sheet: 0.38 (0.19), residues: 734 loop : -0.96 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 577 TYR 0.019 0.001 TYR B1067 PHE 0.014 0.001 PHE C 898 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00285 (26958) covalent geometry : angle 0.50477 (36659) SS BOND : bond 0.00423 ( 44) SS BOND : angle 1.45337 ( 88) hydrogen bonds : bond 0.04143 ( 1048) hydrogen bonds : angle 5.61179 ( 3024) Misc. bond : bond 0.00027 ( 15) link_BETA1-4 : bond 0.00238 ( 9) link_BETA1-4 : angle 1.18480 ( 27) link_NAG-ASN : bond 0.00428 ( 30) link_NAG-ASN : angle 2.63809 ( 90) link_TRANS : bond 0.00154 ( 3) link_TRANS : angle 0.14535 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 97 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 286 THR cc_start: 0.4908 (m) cc_final: 0.4530 (p) REVERT: B 523 THR cc_start: 0.7895 (p) cc_final: 0.7558 (t) REVERT: B 661 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: B 755 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: C 177 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.5983 (ttt) REVERT: C 985 ASP cc_start: 0.7364 (p0) cc_final: 0.7085 (p0) REVERT: C 988 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: C 1142 GLN cc_start: 0.8761 (pp30) cc_final: 0.8427 (pp30) outliers start: 68 outliers final: 42 residues processed: 160 average time/residue: 0.6160 time to fit residues: 118.6493 Evaluate side-chains 140 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 94 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 208 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 316 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 292 optimal weight: 0.1980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 165 ASN C1054 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076961 restraints weight = 44747.858| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.19 r_work: 0.3011 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27059 Z= 0.162 Angle : 0.556 13.317 36873 Z= 0.282 Chirality : 0.044 0.194 4252 Planarity : 0.004 0.066 4686 Dihedral : 6.154 59.675 4441 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.44 % Allowed : 18.06 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: 0.02 (0.14), residues: 3223 helix: 1.93 (0.20), residues: 698 sheet: 0.37 (0.19), residues: 748 loop : -0.95 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE C 898 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00382 (26958) covalent geometry : angle 0.53400 (36659) SS BOND : bond 0.00427 ( 44) SS BOND : angle 1.66236 ( 88) hydrogen bonds : bond 0.04489 ( 1048) hydrogen bonds : angle 5.66995 ( 3024) Misc. bond : bond 0.00030 ( 15) link_BETA1-4 : bond 0.00171 ( 9) link_BETA1-4 : angle 1.28812 ( 27) link_NAG-ASN : bond 0.00436 ( 30) link_NAG-ASN : angle 2.72469 ( 90) link_TRANS : bond 0.00216 ( 3) link_TRANS : angle 0.12789 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 97 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 516 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: B 661 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: B 755 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: C 177 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6025 (ttt) REVERT: C 469 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7878 (p) REVERT: C 528 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7853 (mttp) REVERT: C 985 ASP cc_start: 0.7373 (p0) cc_final: 0.7146 (p0) REVERT: C 988 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: C 1142 GLN cc_start: 0.8766 (pp30) cc_final: 0.8382 (pp30) outliers start: 70 outliers final: 49 residues processed: 161 average time/residue: 0.5875 time to fit residues: 113.6662 Evaluate side-chains 150 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 94 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 27 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 285 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.106851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075858 restraints weight = 45247.319| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.20 r_work: 0.2989 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27059 Z= 0.223 Angle : 0.599 14.249 36873 Z= 0.304 Chirality : 0.046 0.200 4252 Planarity : 0.004 0.066 4686 Dihedral : 6.254 58.294 4437 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.44 % Allowed : 18.30 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: -0.04 (0.14), residues: 3223 helix: 1.83 (0.20), residues: 698 sheet: 0.37 (0.19), residues: 750 loop : -0.99 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1039 TYR 0.021 0.002 TYR B1067 PHE 0.017 0.001 PHE A 898 TRP 0.008 0.001 TRP C 258 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00534 (26958) covalent geometry : angle 0.57406 (36659) SS BOND : bond 0.00467 ( 44) SS BOND : angle 1.90312 ( 88) hydrogen bonds : bond 0.04950 ( 1048) hydrogen bonds : angle 5.79780 ( 3024) Misc. bond : bond 0.00052 ( 15) link_BETA1-4 : bond 0.00146 ( 9) link_BETA1-4 : angle 1.41215 ( 27) link_NAG-ASN : bond 0.00479 ( 30) link_NAG-ASN : angle 2.90822 ( 90) link_TRANS : bond 0.00303 ( 3) link_TRANS : angle 0.12707 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 96 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 523 THR cc_start: 0.8156 (p) cc_final: 0.7841 (p) REVERT: B 516 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: B 661 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: B 755 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: C 177 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6206 (ttt) REVERT: C 469 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7830 (p) REVERT: C 528 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7818 (mttp) REVERT: C 780 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: C 985 ASP cc_start: 0.7433 (p0) cc_final: 0.7187 (p0) REVERT: C 988 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: C 1142 GLN cc_start: 0.8788 (pp30) cc_final: 0.8380 (pp30) outliers start: 70 outliers final: 53 residues processed: 160 average time/residue: 0.5313 time to fit residues: 102.4089 Evaluate side-chains 155 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 94 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 52 optimal weight: 0.4980 chunk 164 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 316 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 123 optimal weight: 0.0070 chunk 259 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN B 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079520 restraints weight = 45121.853| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.21 r_work: 0.3063 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27059 Z= 0.095 Angle : 0.508 12.103 36873 Z= 0.259 Chirality : 0.043 0.188 4252 Planarity : 0.004 0.066 4686 Dihedral : 5.795 59.057 4437 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.70 % Allowed : 19.21 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: 0.15 (0.15), residues: 3223 helix: 2.03 (0.20), residues: 699 sheet: 0.50 (0.19), residues: 726 loop : -0.88 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 577 TYR 0.019 0.001 TYR B1067 PHE 0.011 0.001 PHE C1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00205 (26958) covalent geometry : angle 0.49111 (36659) SS BOND : bond 0.00371 ( 44) SS BOND : angle 1.16096 ( 88) hydrogen bonds : bond 0.03704 ( 1048) hydrogen bonds : angle 5.43096 ( 3024) Misc. bond : bond 0.00178 ( 15) link_BETA1-4 : bond 0.00315 ( 9) link_BETA1-4 : angle 1.03435 ( 27) link_NAG-ASN : bond 0.00433 ( 30) link_NAG-ASN : angle 2.43225 ( 90) link_TRANS : bond 0.00087 ( 3) link_TRANS : angle 0.17326 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 102 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.7900 (p) cc_final: 0.7526 (t) REVERT: B 286 THR cc_start: 0.4836 (m) cc_final: 0.4449 (p) REVERT: B 516 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: B 523 THR cc_start: 0.7801 (p) cc_final: 0.7507 (t) REVERT: B 661 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: C 165 ASN cc_start: 0.3892 (m110) cc_final: 0.3624 (m-40) REVERT: C 177 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.5982 (ttt) REVERT: C 985 ASP cc_start: 0.7300 (p0) cc_final: 0.7038 (p0) REVERT: C 988 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: C 1142 GLN cc_start: 0.8790 (pp30) cc_final: 0.8474 (pp30) outliers start: 49 outliers final: 29 residues processed: 148 average time/residue: 0.5790 time to fit residues: 102.7832 Evaluate side-chains 128 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 314 optimal weight: 0.0980 chunk 315 optimal weight: 0.0470 chunk 25 optimal weight: 8.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079431 restraints weight = 44986.941| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.21 r_work: 0.3063 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 27059 Z= 0.129 Angle : 0.694 61.593 36873 Z= 0.348 Chirality : 0.043 0.392 4252 Planarity : 0.004 0.146 4686 Dihedral : 5.667 59.061 4428 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.36 % Allowed : 19.52 % Favored : 79.12 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: 0.16 (0.14), residues: 3223 helix: 2.02 (0.20), residues: 699 sheet: 0.51 (0.19), residues: 726 loop : -0.87 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 577 TYR 0.019 0.001 TYR B1067 PHE 0.011 0.001 PHE C1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00288 (26958) covalent geometry : angle 0.66844 (36659) SS BOND : bond 0.01596 ( 44) SS BOND : angle 3.02649 ( 88) hydrogen bonds : bond 0.03723 ( 1048) hydrogen bonds : angle 5.42990 ( 3024) Misc. bond : bond 0.00011 ( 15) link_BETA1-4 : bond 0.00360 ( 9) link_BETA1-4 : angle 1.05574 ( 27) link_NAG-ASN : bond 0.00427 ( 30) link_NAG-ASN : angle 2.43346 ( 90) link_TRANS : bond 0.00110 ( 3) link_TRANS : angle 0.17567 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.7912 (p) cc_final: 0.7536 (t) REVERT: B 286 THR cc_start: 0.4842 (m) cc_final: 0.4452 (p) REVERT: B 516 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: B 523 THR cc_start: 0.7811 (p) cc_final: 0.7521 (t) REVERT: B 661 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: C 165 ASN cc_start: 0.3901 (m110) cc_final: 0.3635 (m-40) REVERT: C 177 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5971 (ttt) REVERT: C 979 ASP cc_start: 0.7963 (t70) cc_final: 0.7275 (t0) REVERT: C 985 ASP cc_start: 0.7302 (p0) cc_final: 0.7043 (p0) REVERT: C 988 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: C 1142 GLN cc_start: 0.8794 (pp30) cc_final: 0.8480 (pp30) outliers start: 39 outliers final: 30 residues processed: 131 average time/residue: 0.6299 time to fit residues: 99.3856 Evaluate side-chains 129 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 57 optimal weight: 9.9990 chunk 44 optimal weight: 0.2980 chunk 6 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 259 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079433 restraints weight = 44857.343| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.20 r_work: 0.3063 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 27059 Z= 0.135 Angle : 0.694 61.593 36873 Z= 0.348 Chirality : 0.043 0.392 4252 Planarity : 0.004 0.146 4686 Dihedral : 5.667 59.061 4428 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.22 % Allowed : 19.59 % Favored : 79.19 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: 0.16 (0.14), residues: 3223 helix: 2.02 (0.20), residues: 699 sheet: 0.51 (0.19), residues: 726 loop : -0.87 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 577 TYR 0.019 0.001 TYR B1067 PHE 0.011 0.001 PHE C1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00288 (26958) covalent geometry : angle 0.66844 (36659) SS BOND : bond 0.02524 ( 44) SS BOND : angle 3.08172 ( 88) hydrogen bonds : bond 0.03723 ( 1048) hydrogen bonds : angle 5.42990 ( 3024) Misc. bond : bond 0.00011 ( 15) link_BETA1-4 : bond 0.00360 ( 9) link_BETA1-4 : angle 1.05574 ( 27) link_NAG-ASN : bond 0.00427 ( 30) link_NAG-ASN : angle 2.43346 ( 90) link_TRANS : bond 0.00110 ( 3) link_TRANS : angle 0.17567 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11755.69 seconds wall clock time: 200 minutes 41.74 seconds (12041.74 seconds total)