Starting phenix.real_space_refine on Mon Jun 23 01:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gxe_51659/06_2025/9gxe_51659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gxe_51659/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gxe_51659/06_2025/9gxe_51659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gxe_51659/06_2025/9gxe_51659.map" model { file = "/net/cci-nas-00/data/ceres_data/9gxe_51659/06_2025/9gxe_51659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gxe_51659/06_2025/9gxe_51659.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.54, per 1000 atoms: 0.62 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: 6.78 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 4.17 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: 12.47 Time building geometry restraints manager: 7.96 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 1145 or resid 1201 through 12 \ 06)) 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 1145 or resid 1201 through 12 \ 06)) selection = (chain 'C' and (resid 14 through 1145 or resid 1201 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 63.790 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:25.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.002 TRP B 64 HIS 0.002 0.001 HIS A 66 PHE 0.017 0.002 PHE B 238 TYR 0.026 0.002 TYR A1067 ARG 0.013 0.000 ARG A 357 Details of bonding type rmsd link_TRANS : bond 0.00214 ( 3) link_TRANS : angle 0.34416 ( 9) link_NAG-ASN : bond 0.00615 ( 30) link_NAG-ASN : angle 3.54395 ( 90) link_BETA1-4 : bond 0.00653 ( 9) link_BETA1-4 : angle 1.50901 ( 27) hydrogen bonds : bond 0.11188 ( 1048) hydrogen bonds : angle 7.42551 ( 3024) SS BOND : bond 0.00600 ( 44) SS BOND : angle 1.83747 ( 88) covalent geometry : bond 0.00544 (26958) covalent geometry : angle 0.76100 (36659) Misc. bond : bond 0.11286 ( 15) *********************** 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 : 3.021 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: 0.9763 time to fit residues: 214.4346 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 : 2.780 ------------------------------------------------------------------------------- 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 273 optimal weight: 9.9990 chunk 245 optimal weight: 0.0870 chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 0.1980 chunk 189 optimal weight: 3.9990 chunk 294 optimal weight: 0.4980 overall best weight: 0.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 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 = 0.3699 r_free = 0.3699 target = 0.110459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079858 restraints weight = 45149.741| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.20 r_work: 0.3073 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 27059 Z= 0.098 Angle : 0.518 13.631 36873 Z= 0.267 Chirality : 0.042 0.179 4252 Planarity : 0.005 0.073 4686 Dihedral : 7.861 58.937 4524 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.71 % Allowed : 17.75 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3223 helix: 1.33 (0.20), residues: 709 sheet: 0.41 (0.18), residues: 732 loop : -1.13 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS B 66 PHE 0.012 0.001 PHE C 898 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd link_TRANS : bond 0.00009 ( 3) link_TRANS : angle 0.26415 ( 9) link_NAG-ASN : bond 0.00441 ( 30) link_NAG-ASN : angle 2.66400 ( 90) link_BETA1-4 : bond 0.00335 ( 9) link_BETA1-4 : angle 1.13017 ( 27) hydrogen bonds : bond 0.04083 ( 1048) hydrogen bonds : angle 5.95228 ( 3024) SS BOND : bond 0.00359 ( 44) SS BOND : angle 1.22952 ( 88) covalent geometry : bond 0.00208 (26958) covalent geometry : angle 0.49738 (36659) Misc. bond : bond 0.00026 ( 15) *********************** 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 176 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 98 time to evaluate : 2.789 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6298 (mmm) cc_final: 0.6019 (mmt) REVERT: A 523 THR cc_start: 0.8204 (p) cc_final: 0.7921 (p) REVERT: A 902 MET cc_start: 0.8999 (tpp) cc_final: 0.8693 (tpp) REVERT: B 988 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8220 (mt-10) REVERT: C 177 MET cc_start: 0.6469 (ttt) cc_final: 0.5521 (ttt) outliers start: 78 outliers final: 46 residues processed: 173 average time/residue: 1.0745 time to fit residues: 227.2815 Evaluate side-chains 133 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 2.778 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR 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 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 979 ASP 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 A residue 1141 LEU 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 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 604 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 29 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 319 ARG 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 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 Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 210 optimal weight: 0.1980 chunk 313 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 294 optimal weight: 0.5980 chunk 248 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 297 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 607 GLN B 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.109824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079107 restraints weight = 45011.803| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.20 r_work: 0.3057 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0738 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= 0.117 Angle : 0.517 12.316 36873 Z= 0.264 Chirality : 0.043 0.176 4252 Planarity : 0.004 0.068 4686 Dihedral : 6.918 55.604 4469 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.54 % Allowed : 17.92 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3223 helix: 1.77 (0.20), residues: 698 sheet: 0.41 (0.18), residues: 733 loop : -1.02 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS C 66 PHE 0.012 0.001 PHE C 898 TYR 0.021 0.001 TYR C1067 ARG 0.002 0.000 ARG B 577 Details of bonding type rmsd link_TRANS : bond 0.00151 ( 3) link_TRANS : angle 0.13139 ( 9) link_NAG-ASN : bond 0.00419 ( 30) link_NAG-ASN : angle 2.51882 ( 90) link_BETA1-4 : bond 0.00245 ( 9) link_BETA1-4 : angle 1.18812 ( 27) hydrogen bonds : bond 0.04085 ( 1048) hydrogen bonds : angle 5.70901 ( 3024) SS BOND : bond 0.00344 ( 44) SS BOND : angle 1.29458 ( 88) covalent geometry : bond 0.00265 (26958) covalent geometry : angle 0.49832 (36659) Misc. bond : bond 0.00015 ( 15) *********************** 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 168 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 95 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6605 (mt) REVERT: A 523 THR cc_start: 0.8138 (p) cc_final: 0.7849 (p) REVERT: B 988 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8279 (mt-10) REVERT: C 177 MET cc_start: 0.6353 (ttt) cc_final: 0.5551 (ttt) REVERT: C 988 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7982 (pm20) outliers start: 73 outliers final: 44 residues processed: 162 average time/residue: 1.1449 time to fit residues: 226.0245 Evaluate side-chains 137 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 2.997 ------------------------------------------------------------------------------- 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 270 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR 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 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU 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 875 SER 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 63 THR 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 319 ARG 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 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 979 ASP 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 183 optimal weight: 0.3980 chunk 94 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 27 optimal weight: 0.0270 chunk 48 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 chunk 233 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.110542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079881 restraints weight = 45360.082| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.22 r_work: 0.3074 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27059 Z= 0.097 Angle : 0.490 11.064 36873 Z= 0.250 Chirality : 0.042 0.180 4252 Planarity : 0.004 0.067 4686 Dihedral : 6.131 54.602 4454 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.26 % Allowed : 17.85 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3223 helix: 2.02 (0.20), residues: 697 sheet: 0.47 (0.18), residues: 726 loop : -0.95 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.000 HIS C 66 PHE 0.012 0.001 PHE C 898 TYR 0.020 0.001 TYR B1067 ARG 0.002 0.000 ARG B 577 Details of bonding type rmsd link_TRANS : bond 0.00091 ( 3) link_TRANS : angle 0.16174 ( 9) link_NAG-ASN : bond 0.00405 ( 30) link_NAG-ASN : angle 2.30708 ( 90) link_BETA1-4 : bond 0.00275 ( 9) link_BETA1-4 : angle 1.11229 ( 27) hydrogen bonds : bond 0.03750 ( 1048) hydrogen bonds : angle 5.44821 ( 3024) SS BOND : bond 0.00338 ( 44) SS BOND : angle 1.16797 ( 88) covalent geometry : bond 0.00215 (26958) covalent geometry : angle 0.47318 (36659) Misc. bond : bond 0.00010 ( 15) *********************** 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 162 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 97 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5810 (mmm) cc_final: 0.5606 (mmt) REVERT: A 270 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6612 (mt) REVERT: A 523 THR cc_start: 0.8037 (p) cc_final: 0.7621 (t) REVERT: B 286 THR cc_start: 0.4857 (m) cc_final: 0.4440 (p) REVERT: B 661 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: B 988 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8228 (mt-10) REVERT: C 177 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5596 (ttt) outliers start: 65 outliers final: 36 residues processed: 158 average time/residue: 1.4259 time to fit residues: 275.8199 Evaluate side-chains 127 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 5.416 ------------------------------------------------------------------------------- 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 270 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 825 LYS 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 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 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1141 LEU 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 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 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 300 optimal weight: 0.5980 chunk 137 optimal weight: 0.0170 chunk 10 optimal weight: 9.9990 overall best weight: 3.5224 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.106565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.075466 restraints weight = 45187.701| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.20 r_work: 0.2981 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 27059 Z= 0.274 Angle : 0.624 13.874 36873 Z= 0.318 Chirality : 0.048 0.192 4252 Planarity : 0.004 0.065 4686 Dihedral : 6.437 58.890 4441 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.33 % Allowed : 17.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3223 helix: 1.76 (0.20), residues: 697 sheet: 0.35 (0.18), residues: 760 loop : -1.01 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 104 HIS 0.004 0.001 HIS C 66 PHE 0.018 0.002 PHE B 898 TYR 0.021 0.002 TYR B1067 ARG 0.004 0.001 ARG A1000 Details of bonding type rmsd link_TRANS : bond 0.00348 ( 3) link_TRANS : angle 0.11157 ( 9) link_NAG-ASN : bond 0.00509 ( 30) link_NAG-ASN : angle 2.95028 ( 90) link_BETA1-4 : bond 0.00329 ( 9) link_BETA1-4 : angle 1.52464 ( 27) hydrogen bonds : bond 0.05311 ( 1048) hydrogen bonds : angle 5.87996 ( 3024) SS BOND : bond 0.00478 ( 44) SS BOND : angle 1.90553 ( 88) covalent geometry : bond 0.00663 (26958) covalent geometry : angle 0.59977 (36659) Misc. bond : bond 0.00046 ( 15) *********************** 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 159 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 92 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.8142 (p) cc_final: 0.7853 (p) REVERT: B 661 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: B 755 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: C 177 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.5898 (ttt) REVERT: C 985 ASP cc_start: 0.7457 (p0) cc_final: 0.6769 (p0) REVERT: C 988 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7999 (mp0) outliers start: 67 outliers final: 47 residues processed: 154 average time/residue: 1.0747 time to fit residues: 203.3000 Evaluate side-chains 139 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 88 time to evaluate : 2.973 ------------------------------------------------------------------------------- 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 277 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 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 747 THR 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 16 VAL 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 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 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN 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 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 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 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 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 851 CYS 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 81 optimal weight: 0.0870 chunk 79 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 237 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 303 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.109102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078380 restraints weight = 44975.621| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.20 r_work: 0.3042 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27059 Z= 0.107 Angle : 0.516 12.209 36873 Z= 0.263 Chirality : 0.043 0.195 4252 Planarity : 0.004 0.067 4686 Dihedral : 5.976 55.799 4440 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.02 % Allowed : 18.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3223 helix: 1.99 (0.20), residues: 697 sheet: 0.46 (0.19), residues: 729 loop : -0.94 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS C 66 PHE 0.012 0.001 PHE C 898 TYR 0.019 0.001 TYR B1067 ARG 0.002 0.000 ARG B 577 Details of bonding type rmsd link_TRANS : bond 0.00120 ( 3) link_TRANS : angle 0.16486 ( 9) link_NAG-ASN : bond 0.00419 ( 30) link_NAG-ASN : angle 2.54786 ( 90) link_BETA1-4 : bond 0.00296 ( 9) link_BETA1-4 : angle 1.11846 ( 27) hydrogen bonds : bond 0.04024 ( 1048) hydrogen bonds : angle 5.56155 ( 3024) SS BOND : bond 0.00392 ( 44) SS BOND : angle 1.39342 ( 88) covalent geometry : bond 0.00236 (26958) covalent geometry : angle 0.49659 (36659) Misc. bond : bond 0.00012 ( 15) *********************** 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 152 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 94 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.8053 (p) cc_final: 0.7638 (t) REVERT: B 286 THR cc_start: 0.4881 (m) cc_final: 0.4491 (p) REVERT: B 661 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 988 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8213 (mt-10) REVERT: C 177 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5758 (ttt) REVERT: C 469 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7948 (p) REVERT: C 480 CYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6445 (m) REVERT: C 985 ASP cc_start: 0.7372 (p0) cc_final: 0.6797 (p0) REVERT: C 988 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7997 (mp0) outliers start: 58 outliers final: 35 residues processed: 148 average time/residue: 1.1817 time to fit residues: 212.0992 Evaluate side-chains 131 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 3.165 ------------------------------------------------------------------------------- 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 315 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 776 LYS 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 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 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 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1144 GLU 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 315 THR Chi-restraints excluded: chain C residue 319 ARG 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 827 THR Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 979 ASP 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 323 optimal weight: 0.8980 chunk 292 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077505 restraints weight = 45095.407| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.21 r_work: 0.3022 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27059 Z= 0.142 Angle : 0.535 11.964 36873 Z= 0.272 Chirality : 0.044 0.191 4252 Planarity : 0.004 0.064 4686 Dihedral : 5.873 56.421 4438 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.23 % Allowed : 18.13 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3223 helix: 2.01 (0.20), residues: 697 sheet: 0.45 (0.19), residues: 739 loop : -0.95 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.003 0.001 HIS C 66 PHE 0.015 0.001 PHE C 898 TYR 0.020 0.001 TYR B1067 ARG 0.002 0.000 ARG A1000 Details of bonding type rmsd link_TRANS : bond 0.00184 ( 3) link_TRANS : angle 0.12469 ( 9) link_NAG-ASN : bond 0.00412 ( 30) link_NAG-ASN : angle 2.57596 ( 90) link_BETA1-4 : bond 0.00195 ( 9) link_BETA1-4 : angle 1.24287 ( 27) hydrogen bonds : bond 0.04276 ( 1048) hydrogen bonds : angle 5.56065 ( 3024) SS BOND : bond 0.00410 ( 44) SS BOND : angle 1.48866 ( 88) covalent geometry : bond 0.00333 (26958) covalent geometry : angle 0.51505 (36659) Misc. bond : bond 0.00019 ( 15) *********************** 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 158 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 94 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.8026 (p) cc_final: 0.7616 (t) REVERT: B 286 THR cc_start: 0.4906 (m) cc_final: 0.4523 (p) REVERT: B 661 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: B 1142 GLN cc_start: 0.8742 (pp30) cc_final: 0.8401 (pp30) REVERT: C 177 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5819 (ttt) REVERT: C 469 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7909 (p) REVERT: C 480 CYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6527 (m) REVERT: C 985 ASP cc_start: 0.7334 (p0) cc_final: 0.6735 (p0) REVERT: C 988 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: C 1142 GLN cc_start: 0.8738 (pp30) cc_final: 0.8464 (pp30) outliers start: 64 outliers final: 43 residues processed: 152 average time/residue: 1.3803 time to fit residues: 257.2743 Evaluate side-chains 140 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 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 315 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 825 LYS 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 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 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 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 875 SER Chi-restraints excluded: chain B residue 977 LEU 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 373 SER 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 828 LEU Chi-restraints excluded: chain C residue 851 CYS 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 308 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 0.2980 chunk 254 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 301 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN C1054 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078024 restraints weight = 45246.757| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.22 r_work: 0.3031 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27059 Z= 0.123 Angle : 0.526 11.705 36873 Z= 0.267 Chirality : 0.043 0.193 4252 Planarity : 0.004 0.065 4686 Dihedral : 5.760 55.995 4436 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.23 % Allowed : 18.06 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3223 helix: 2.03 (0.20), residues: 697 sheet: 0.44 (0.19), residues: 730 loop : -0.92 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS C 66 PHE 0.014 0.001 PHE C 898 TYR 0.019 0.001 TYR B1067 ARG 0.001 0.000 ARG B 577 Details of bonding type rmsd link_TRANS : bond 0.00158 ( 3) link_TRANS : angle 0.13632 ( 9) link_NAG-ASN : bond 0.00404 ( 30) link_NAG-ASN : angle 2.51715 ( 90) link_BETA1-4 : bond 0.00232 ( 9) link_BETA1-4 : angle 1.18445 ( 27) hydrogen bonds : bond 0.04115 ( 1048) hydrogen bonds : angle 5.51780 ( 3024) SS BOND : bond 0.00387 ( 44) SS BOND : angle 1.56261 ( 88) covalent geometry : bond 0.00285 (26958) covalent geometry : angle 0.50584 (36659) Misc. bond : bond 0.00028 ( 15) *********************** 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 159 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 95 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6737 (mt) REVERT: A 523 THR cc_start: 0.7979 (p) cc_final: 0.7593 (t) REVERT: B 286 THR cc_start: 0.4894 (m) cc_final: 0.4507 (p) REVERT: B 661 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: B 1142 GLN cc_start: 0.8753 (pp30) cc_final: 0.8399 (pp30) REVERT: B 1144 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6788 (pt0) REVERT: C 177 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5785 (ttt) REVERT: C 469 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7908 (p) REVERT: C 480 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6516 (m) REVERT: C 985 ASP cc_start: 0.7313 (p0) cc_final: 0.6717 (p0) REVERT: C 988 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: C 1142 GLN cc_start: 0.8728 (pp30) cc_final: 0.8454 (pp30) outliers start: 64 outliers final: 47 residues processed: 155 average time/residue: 1.0823 time to fit residues: 204.3244 Evaluate side-chains 147 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 93 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 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 270 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 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 747 THR 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 A residue 1141 LEU 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 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 597 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1144 GLU 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 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 851 CYS 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 142 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077388 restraints weight = 45240.499| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.22 r_work: 0.3020 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27059 Z= 0.151 Angle : 0.544 11.892 36873 Z= 0.277 Chirality : 0.044 0.192 4252 Planarity : 0.004 0.064 4686 Dihedral : 5.784 56.527 4436 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.19 % Allowed : 18.13 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3223 helix: 2.00 (0.20), residues: 698 sheet: 0.45 (0.19), residues: 739 loop : -0.95 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.003 0.001 HIS C 66 PHE 0.015 0.001 PHE C 898 TYR 0.020 0.001 TYR B1067 ARG 0.002 0.000 ARG A1000 Details of bonding type rmsd link_TRANS : bond 0.00199 ( 3) link_TRANS : angle 0.13127 ( 9) link_NAG-ASN : bond 0.00412 ( 30) link_NAG-ASN : angle 2.58393 ( 90) link_BETA1-4 : bond 0.00195 ( 9) link_BETA1-4 : angle 1.25236 ( 27) hydrogen bonds : bond 0.04345 ( 1048) hydrogen bonds : angle 5.57125 ( 3024) SS BOND : bond 0.00416 ( 44) SS BOND : angle 1.62215 ( 88) covalent geometry : bond 0.00356 (26958) covalent geometry : angle 0.52331 (36659) Misc. bond : bond 0.00022 ( 15) *********************** 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 157 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 94 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6870 (mt) REVERT: A 523 THR cc_start: 0.7998 (p) cc_final: 0.7598 (t) REVERT: B 661 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: B 1142 GLN cc_start: 0.8743 (pp30) cc_final: 0.8377 (pp30) REVERT: C 177 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5807 (ttt) REVERT: C 469 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7892 (p) REVERT: C 480 CYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6563 (m) REVERT: C 985 ASP cc_start: 0.7317 (p0) cc_final: 0.6737 (p0) REVERT: C 988 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: C 1142 GLN cc_start: 0.8738 (pp30) cc_final: 0.8434 (pp30) outliers start: 63 outliers final: 49 residues processed: 152 average time/residue: 1.2002 time to fit residues: 228.2488 Evaluate side-chains 148 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 93 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 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 270 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 576 VAL 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 747 THR 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 916 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU 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 240 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 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 977 LEU 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 277 LEU Chi-restraints excluded: chain C residue 315 THR 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 828 LEU Chi-restraints excluded: chain C residue 851 CYS 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 295 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 271 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.108493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.077659 restraints weight = 44851.516| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.19 r_work: 0.3027 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27059 Z= 0.141 Angle : 0.538 11.815 36873 Z= 0.273 Chirality : 0.044 0.191 4252 Planarity : 0.004 0.064 4686 Dihedral : 5.677 56.314 4431 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.12 % Allowed : 18.30 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3223 helix: 2.00 (0.20), residues: 698 sheet: 0.42 (0.19), residues: 736 loop : -0.94 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS C 66 PHE 0.014 0.001 PHE C 898 TYR 0.020 0.001 TYR B1067 ARG 0.002 0.000 ARG A1000 Details of bonding type rmsd link_TRANS : bond 0.00185 ( 3) link_TRANS : angle 0.13211 ( 9) link_NAG-ASN : bond 0.00405 ( 30) link_NAG-ASN : angle 2.56116 ( 90) link_BETA1-4 : bond 0.00202 ( 9) link_BETA1-4 : angle 1.21623 ( 27) hydrogen bonds : bond 0.04259 ( 1048) hydrogen bonds : angle 5.55072 ( 3024) SS BOND : bond 0.00415 ( 44) SS BOND : angle 1.55026 ( 88) covalent geometry : bond 0.00329 (26958) covalent geometry : angle 0.51735 (36659) Misc. bond : bond 0.00023 ( 15) ********************** 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 154 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 93 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6873 (mt) REVERT: A 523 THR cc_start: 0.7996 (p) cc_final: 0.7607 (t) REVERT: B 286 THR cc_start: 0.4924 (m) cc_final: 0.4537 (p) REVERT: B 661 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: B 1142 GLN cc_start: 0.8748 (pp30) cc_final: 0.8423 (pp30) REVERT: B 1144 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6670 (pt0) REVERT: C 177 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.5802 (ttt) REVERT: C 469 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7900 (p) REVERT: C 480 CYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6563 (m) REVERT: C 516 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: C 985 ASP cc_start: 0.7319 (p0) cc_final: 0.6748 (p0) REVERT: C 988 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: C 1142 GLN cc_start: 0.8727 (pp30) cc_final: 0.8429 (pp30) outliers start: 61 outliers final: 48 residues processed: 147 average time/residue: 1.1828 time to fit residues: 210.9472 Evaluate side-chains 149 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 93 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 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 270 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 747 THR 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 916 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 16 VAL 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 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 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1144 GLU 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 373 SER 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 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 851 CYS 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 157 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077536 restraints weight = 44997.052| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.21 r_work: 0.3024 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27059 Z= 0.145 Angle : 0.540 11.828 36873 Z= 0.274 Chirality : 0.044 0.192 4252 Planarity : 0.004 0.064 4686 Dihedral : 5.576 56.379 4426 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.12 % Allowed : 18.44 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3223 helix: 2.00 (0.20), residues: 698 sheet: 0.42 (0.19), residues: 736 loop : -0.94 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 258 HIS 0.003 0.001 HIS C 66 PHE 0.015 0.001 PHE C 898 TYR 0.020 0.001 TYR B1067 ARG 0.002 0.000 ARG A1000 Details of bonding type rmsd link_TRANS : bond 0.00192 ( 3) link_TRANS : angle 0.12876 ( 9) link_NAG-ASN : bond 0.00406 ( 30) link_NAG-ASN : angle 2.57033 ( 90) link_BETA1-4 : bond 0.00218 ( 9) link_BETA1-4 : angle 1.23426 ( 27) hydrogen bonds : bond 0.04285 ( 1048) hydrogen bonds : angle 5.55376 ( 3024) SS BOND : bond 0.00415 ( 44) SS BOND : angle 1.54687 ( 88) covalent geometry : bond 0.00340 (26958) covalent geometry : angle 0.51960 (36659) Misc. bond : bond 0.00020 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27975.30 seconds wall clock time: 489 minutes 22.83 seconds (29362.83 seconds total)