Starting phenix.real_space_refine on Sun Jul 5 19:59:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8heb_34686/07_2026/8heb_34686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8heb_34686/07_2026/8heb_34686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8heb_34686/07_2026/8heb_34686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8heb_34686/07_2026/8heb_34686.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8heb_34686/07_2026/8heb_34686.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8heb_34686/07_2026/8heb_34686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8heb_34686/07_2026/8heb_34686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8heb_34686/07_2026/8heb_34686.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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 141 5.16 5 C 18981 2.51 5 N 4895 2.21 5 O 5895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29912 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7980 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7982 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 7 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 7974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7974 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 51, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "G" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "H" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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 chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "a" 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 chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.99, per 1000 atoms: 0.20 Number of scatterers: 29912 At special positions: 0 Unit cell: (154.98, 147.6, 217.3, 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 141 16.00 O 5895 8.00 N 4895 7.00 C 18981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6998 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 69 sheets defined 21.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.593A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.768A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.511A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.982A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.590A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.655A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.532A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.107A 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: 4.588A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.895A 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 1032 removed outlier: 4.236A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.537A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.593A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.088A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.773A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.068A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.284A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.685A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.512A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.911A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.627A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.787A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.149A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 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: 4.155A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.081A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.710A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.191A 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 removed outlier: 3.968A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.382A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.794A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.937A pdb=" N ALA D 82 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.939A pdb=" N ALA F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'H' and resid 78 through 82 removed outlier: 3.914A pdb=" N ALA H 82 " --> pdb=" O CYS H 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.808A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.575A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.524A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.444A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.859A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.709A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.386A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.091A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.720A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.416A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.619A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.060A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.172A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 132 through 135 removed outlier: 6.717A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 141 through 142 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 318 through 319 Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.146A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.432A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.272A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.875A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.621A 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 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.541A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.084A 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 Processing sheet with id=AE4, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.909A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.345A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.447A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.882A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.144A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.975A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.586A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.544A pdb=" N VAL D 18 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.598A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D 47 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.598A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY D 89 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 100 " --> pdb=" O GLY D 89 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.972A pdb=" N LEU E 17 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET E 79 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.534A pdb=" N SER E 34 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.508A pdb=" N VAL F 18 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.603A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS F 110 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AG8, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.898A pdb=" N LEU G 17 " --> pdb=" O MET G 79 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 79 " --> pdb=" O LEU G 17 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.880A pdb=" N MET G 33 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.502A pdb=" N VAL H 18 " --> pdb=" O MET H 74 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS H 69 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.592A pdb=" N VAL H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 12 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE H 47 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN H 36 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU H 45 " --> pdb=" O GLN H 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.592A pdb=" N VAL H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 12 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY H 89 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA H 100 " --> pdb=" O GLY H 89 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.897A pdb=" N LEU I 17 " --> pdb=" O MET I 79 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET I 79 " --> pdb=" O LEU I 17 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.563A pdb=" N GLY I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG I 37 " --> pdb=" O TRP I 46 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TRP I 46 " --> pdb=" O ARG I 37 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.839A pdb=" N PHE I 106 " --> pdb=" O ARG I 94 " (cutoff:3.500A) 1107 hydrogen bonds defined for protein. 2994 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: 8.59 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9524 1.35 - 1.47: 7957 1.47 - 1.60: 12905 1.60 - 1.72: 0 1.72 - 1.84: 177 Bond restraints: 30563 Sorted by residual: bond pdb=" N GLY D 96 " pdb=" CA GLY D 96 " ideal model delta sigma weight residual 1.446 1.475 -0.029 9.50e-03 1.11e+04 9.43e+00 bond pdb=" N CYS D 98 " pdb=" CA CYS D 98 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.23e+00 bond pdb=" N CYS H 98 " pdb=" CA CYS H 98 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.21e+00 bond pdb=" N SER H 92 " pdb=" CA SER H 92 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.09e+00 bond pdb=" N SER H 95 " pdb=" CA SER H 95 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.00e+00 ... (remaining 30558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 40574 1.61 - 3.22: 910 3.22 - 4.83: 94 4.83 - 6.44: 35 6.44 - 8.05: 5 Bond angle restraints: 41618 Sorted by residual: angle pdb=" N ILE H 28 " pdb=" CA ILE H 28 " pdb=" C ILE H 28 " ideal model delta sigma weight residual 113.10 108.16 4.94 9.70e-01 1.06e+00 2.59e+01 angle pdb=" N ILE D 28 " pdb=" CA ILE D 28 " pdb=" C ILE D 28 " ideal model delta sigma weight residual 113.10 108.34 4.76 9.70e-01 1.06e+00 2.41e+01 angle pdb=" N ILE F 28 " pdb=" CA ILE F 28 " pdb=" C ILE F 28 " ideal model delta sigma weight residual 113.10 108.45 4.65 9.70e-01 1.06e+00 2.30e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.53 109.51 4.02 9.80e-01 1.04e+00 1.68e+01 angle pdb=" C SER F 92 " pdb=" CA SER F 92 " pdb=" CB SER F 92 " ideal model delta sigma weight residual 116.63 112.19 4.44 1.16e+00 7.43e-01 1.47e+01 ... (remaining 41613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15743 17.99 - 35.98: 1490 35.98 - 53.98: 288 53.98 - 71.97: 33 71.97 - 89.96: 30 Dihedral angle restraints: 17584 sinusoidal: 6689 harmonic: 10895 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.22 88.22 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -169.32 83.32 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 174.03 -81.03 1 1.00e+01 1.00e-02 8.10e+01 ... (remaining 17581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4927 0.134 - 0.269: 12 0.269 - 0.403: 4 0.403 - 0.538: 0 0.538 - 0.672: 1 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4941 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 81 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C ASN B 81 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 81 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO B 82 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 986 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO B 561 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.026 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 249 2.62 - 3.19: 25525 3.19 - 3.76: 43134 3.76 - 4.33: 57943 4.33 - 4.90: 98907 Nonbonded interactions: 225758 Sorted by model distance: nonbonded pdb=" OD1 ASP A 568 " pdb=" N ILE A 569 " model vdw 2.053 3.120 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.205 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.211 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.221 3.040 ... (remaining 225753 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 15 through 553 or (resid 554 and (name N or name CA or nam \ e C or name O or name CB )) or resid 555 or (resid 556 and (name N or name CA or \ name C or name O or name CB )) or resid 557 through 827 or (resid 854 through 8 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 856 through \ 1309)) selection = (chain 'B' and (resid 15 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 337 or (resid 338 and (name N or n \ ame CA or name C or name O or name CB )) or resid 339 through 555 or (resid 556 \ and (name N or name CA or name C or name O or name CB )) or resid 557 or (resid \ 558 through 559 and (name N or name CA or name C or name O or name CB )) or resi \ d 560 through 785 or (resid 786 and (name N or name CA or name C or name O or na \ me CB )) or resid 787 through 827 or (resid 854 through 855 and (name N or name \ CA or name C or name O or name CB )) or resid 856 through 903 or (resid 904 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2 or name CE1 or name CE2 or name CZ )) or resid 905 through 1309)) selection = (chain 'C' and (resid 15 through 341 or (resid 342 and (name N or name CA or nam \ e C or name O or name CB )) or resid 343 through 553 or (resid 554 and (name N o \ r name CA or name C or name O or name CB )) or resid 555 through 557 or (resid 5 \ 58 through 559 and (name N or name CA or name C or name O or name CB )) or resid \ 560 through 827 or resid 854 through 903 or (resid 904 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or \ name CE2 or name CZ )) or resid 905 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.430 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 : 0.004 0.039 30669 Z= 0.179 Angle : 0.597 14.200 41893 Z= 0.302 Chirality : 0.045 0.672 4944 Planarity : 0.003 0.056 5287 Dihedral : 14.256 89.959 10457 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 0.03 % Allowed : 13.40 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3709 helix: 2.34 (0.22), residues: 635 sheet: 0.01 (0.17), residues: 932 loop : -1.06 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.019 0.001 TYR C 369 PHE 0.024 0.001 PHE A 201 TRP 0.011 0.001 TRP A 104 HIS 0.002 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (30563) covalent geometry : angle 0.57257 / 0.30 (41618) SS BOND : bond 0.00372 / 0.24 ( 43) SS BOND : angle 1.07756 / 0.71 ( 86) hydrogen bonds : bond 0.23448 / 15.56 ( 1076) hydrogen bonds : angle 8.22722 / 5.62 ( 2994) link_BETA1-4 : bond 0.00358 / 0.25 ( 18) link_BETA1-4 : angle 1.09669 / 0.69 ( 54) link_NAG-ASN : bond 0.00444 / 0.29 ( 45) link_NAG-ASN : angle 2.88015 / 2.10 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASN cc_start: 0.8616 (p0) cc_final: 0.7925 (p0) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.1956 time to fit residues: 42.7760 Evaluate side-chains 126 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 751 ASN B 992 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS F 1 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.159903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108357 restraints weight = 70050.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.109078 restraints weight = 42420.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108751 restraints weight = 30176.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109249 restraints weight = 27218.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109455 restraints weight = 25079.007| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30669 Z= 0.127 Angle : 0.552 13.093 41893 Z= 0.282 Chirality : 0.044 0.433 4944 Planarity : 0.003 0.050 5287 Dihedral : 3.813 25.376 4030 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.82 % Rotamer: Outliers : 1.72 % Allowed : 13.50 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3709 helix: 2.10 (0.21), residues: 680 sheet: 0.23 (0.17), residues: 949 loop : -1.03 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.021 0.001 TYR A1067 PHE 0.013 0.001 PHE A 565 TRP 0.020 0.001 TRP A 104 HIS 0.003 0.001 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (30563) covalent geometry : angle 0.52886 / 0.28 (41618) SS BOND : bond 0.00414 / 0.26 ( 43) SS BOND : angle 1.12774 / 0.77 ( 86) hydrogen bonds : bond 0.05114 / 3.37 ( 1076) hydrogen bonds : angle 5.98210 / 4.10 ( 2994) link_BETA1-4 : bond 0.00373 / 0.24 ( 18) link_BETA1-4 : angle 0.94388 / 0.63 ( 54) link_NAG-ASN : bond 0.00461 / 0.30 ( 45) link_NAG-ASN : angle 2.68178 / 1.93 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7702 (OUTLIER) cc_final: 0.7408 (m) REVERT: B 117 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7926 (tt) REVERT: E 30 ARG cc_start: 0.8538 (tpp80) cc_final: 0.8079 (mmp80) REVERT: G 30 ARG cc_start: 0.8489 (tpp80) cc_final: 0.8015 (mmp80) REVERT: G 79 MET cc_start: -0.0524 (pmm) cc_final: -0.0826 (pmm) REVERT: I 30 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8064 (mmp80) REVERT: I 105 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7052 (tm-30) outliers start: 55 outliers final: 26 residues processed: 188 average time/residue: 0.1611 time to fit residues: 51.2456 Evaluate side-chains 153 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 333 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 chunk 301 optimal weight: 6.9990 chunk 341 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 339 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 350 optimal weight: 30.0000 chunk 290 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.158303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106834 restraints weight = 70507.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106248 restraints weight = 45580.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106417 restraints weight = 34166.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107245 restraints weight = 29909.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107311 restraints weight = 25900.627| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 30669 Z= 0.197 Angle : 0.587 13.742 41893 Z= 0.297 Chirality : 0.045 0.421 4944 Planarity : 0.004 0.051 5287 Dihedral : 3.984 26.983 4030 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.80 % Rotamer: Outliers : 2.34 % Allowed : 14.53 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3709 helix: 2.04 (0.21), residues: 673 sheet: 0.21 (0.17), residues: 957 loop : -1.13 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.021 0.001 TYR C1067 PHE 0.015 0.001 PHE B1121 TRP 0.013 0.001 TRP A 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (30563) covalent geometry : angle 0.55972 / 0.29 (41618) SS BOND : bond 0.00403 / 0.25 ( 43) SS BOND : angle 1.79674 / 1.36 ( 86) hydrogen bonds : bond 0.05045 / 3.34 ( 1076) hydrogen bonds : angle 5.57970 / 3.84 ( 2994) link_BETA1-4 : bond 0.00304 / 0.20 ( 18) link_BETA1-4 : angle 0.97791 / 0.65 ( 54) link_NAG-ASN : bond 0.00444 / 0.29 ( 45) link_NAG-ASN : angle 2.80706 / 2.02 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 126 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8143 (ttpp) REVERT: B 117 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8155 (tt) REVERT: C 759 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7803 (t80) REVERT: E 30 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8117 (mmp80) REVERT: E 79 MET cc_start: -0.0232 (pmm) cc_final: -0.0490 (pmm) REVERT: G 79 MET cc_start: -0.0325 (pmm) cc_final: -0.0651 (pmm) REVERT: I 30 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8154 (mmp80) REVERT: I 105 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7079 (tm-30) outliers start: 75 outliers final: 41 residues processed: 195 average time/residue: 0.1605 time to fit residues: 53.1391 Evaluate side-chains 161 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 207 optimal weight: 0.5980 chunk 343 optimal weight: 20.0000 chunk 363 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 357 optimal weight: 40.0000 chunk 61 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.152473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097903 restraints weight = 72936.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100563 restraints weight = 49020.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100431 restraints weight = 34771.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101433 restraints weight = 27966.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.101498 restraints weight = 27964.334| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 30669 Z= 0.152 Angle : 0.550 13.298 41893 Z= 0.278 Chirality : 0.044 0.396 4944 Planarity : 0.003 0.051 5287 Dihedral : 3.948 26.298 4030 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 2.47 % Allowed : 15.78 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3709 helix: 2.01 (0.21), residues: 672 sheet: 0.21 (0.17), residues: 957 loop : -1.12 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.024 0.001 TYR I 102 PHE 0.013 0.001 PHE B1121 TRP 0.011 0.001 TRP A 104 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (30563) covalent geometry : angle 0.52310 / 0.27 (41618) SS BOND : bond 0.00463 / 0.31 ( 43) SS BOND : angle 1.69574 / 1.23 ( 86) hydrogen bonds : bond 0.04539 / 3.01 ( 1076) hydrogen bonds : angle 5.31956 / 3.67 ( 2994) link_BETA1-4 : bond 0.00309 / 0.20 ( 18) link_BETA1-4 : angle 0.96093 / 0.63 ( 54) link_NAG-ASN : bond 0.00419 / 0.27 ( 45) link_NAG-ASN : angle 2.72283 / 1.96 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 126 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.9309 (mp) cc_final: 0.9102 (tt) REVERT: A 503 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7303 (m) REVERT: A 733 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7965 (ttpp) REVERT: B 117 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7957 (tt) REVERT: C 342 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7088 (t80) REVERT: E 79 MET cc_start: -0.0224 (pmm) cc_final: -0.0483 (pmm) REVERT: G 79 MET cc_start: -0.0468 (pmm) cc_final: -0.0728 (pmm) REVERT: I 105 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7374 (tm-30) outliers start: 79 outliers final: 57 residues processed: 199 average time/residue: 0.1616 time to fit residues: 54.5199 Evaluate side-chains 181 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 163 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 361 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 350 optimal weight: 40.0000 chunk 275 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.154962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.113942 restraints weight = 65431.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.108113 restraints weight = 46396.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.108676 restraints weight = 44868.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109018 restraints weight = 32203.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109144 restraints weight = 29982.910| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30669 Z= 0.218 Angle : 0.605 13.939 41893 Z= 0.303 Chirality : 0.045 0.404 4944 Planarity : 0.004 0.051 5287 Dihedral : 4.113 28.622 4030 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.34 % Rotamer: Outliers : 3.56 % Allowed : 15.40 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3709 helix: 1.88 (0.21), residues: 675 sheet: 0.09 (0.17), residues: 958 loop : -1.17 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.022 0.001 TYR B 170 PHE 0.017 0.002 PHE C 377 TRP 0.011 0.001 TRP C 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (30563) covalent geometry : angle 0.57875 / 0.30 (41618) SS BOND : bond 0.00430 / 0.27 ( 43) SS BOND : angle 1.68988 / 1.22 ( 86) hydrogen bonds : bond 0.04964 / 3.29 ( 1076) hydrogen bonds : angle 5.29356 / 3.65 ( 2994) link_BETA1-4 : bond 0.00292 / 0.20 ( 18) link_BETA1-4 : angle 1.01275 / 0.67 ( 54) link_NAG-ASN : bond 0.00450 / 0.29 ( 45) link_NAG-ASN : angle 2.83821 / 2.03 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 129 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.9258 (mp) cc_final: 0.9051 (tt) REVERT: A 369 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: A 503 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7534 (m) REVERT: A 733 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8210 (ttpp) REVERT: A 878 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 117 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8385 (tt) REVERT: C 52 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 342 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7047 (t80) REVERT: E 30 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8090 (mmp80) REVERT: E 79 MET cc_start: 0.0112 (pmm) cc_final: -0.0156 (pmm) REVERT: G 79 MET cc_start: 0.0262 (pmm) cc_final: -0.0067 (pmm) REVERT: I 105 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7261 (tm-30) outliers start: 114 outliers final: 69 residues processed: 234 average time/residue: 0.1609 time to fit residues: 64.4797 Evaluate side-chains 195 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 119 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 71 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 341 optimal weight: 0.4980 chunk 308 optimal weight: 50.0000 chunk 134 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.160063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.104816 restraints weight = 70028.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107928 restraints weight = 40525.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108152 restraints weight = 27791.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108680 restraints weight = 21263.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109370 restraints weight = 19707.790| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30669 Z= 0.152 Angle : 0.567 13.079 41893 Z= 0.281 Chirality : 0.045 0.546 4944 Planarity : 0.003 0.052 5287 Dihedral : 3.993 27.575 4030 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 3.03 % Allowed : 16.46 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3709 helix: 2.03 (0.21), residues: 673 sheet: 0.15 (0.17), residues: 961 loop : -1.12 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 577 TYR 0.023 0.001 TYR B 369 PHE 0.015 0.001 PHE A 392 TRP 0.012 0.001 TRP C 104 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (30563) covalent geometry : angle 0.54303 / 0.28 (41618) SS BOND : bond 0.00417 / 0.26 ( 43) SS BOND : angle 1.53610 / 1.10 ( 86) hydrogen bonds : bond 0.04461 / 2.96 ( 1076) hydrogen bonds : angle 5.11866 / 3.54 ( 2994) link_BETA1-4 : bond 0.00319 / 0.21 ( 18) link_BETA1-4 : angle 1.01582 / 0.66 ( 54) link_NAG-ASN : bond 0.00397 / 0.25 ( 45) link_NAG-ASN : angle 2.65093 / 1.91 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 135 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.9267 (mp) cc_final: 0.9055 (tt) REVERT: A 503 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7409 (m) REVERT: A 733 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7953 (ttpp) REVERT: A 912 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8624 (p) REVERT: B 117 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7959 (tt) REVERT: B 369 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: C 52 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 342 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7138 (t80) REVERT: C 902 MET cc_start: 0.8887 (tpp) cc_final: 0.8486 (tpt) REVERT: I 105 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7367 (tm-30) outliers start: 97 outliers final: 66 residues processed: 223 average time/residue: 0.1556 time to fit residues: 58.9787 Evaluate side-chains 200 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 127 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 117 optimal weight: 5.9990 chunk 357 optimal weight: 50.0000 chunk 194 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 370 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.159450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107599 restraints weight = 70314.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.107437 restraints weight = 44342.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106978 restraints weight = 35204.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107692 restraints weight = 30160.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107868 restraints weight = 26950.419| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30669 Z= 0.212 Angle : 0.607 13.083 41893 Z= 0.302 Chirality : 0.045 0.460 4944 Planarity : 0.004 0.051 5287 Dihedral : 4.108 28.904 4030 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 3.12 % Allowed : 16.84 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3709 helix: 1.92 (0.21), residues: 673 sheet: 0.06 (0.17), residues: 960 loop : -1.17 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.020 0.001 TYR C1067 PHE 0.016 0.002 PHE B1121 TRP 0.012 0.001 TRP C 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (30563) covalent geometry : angle 0.58244 / 0.30 (41618) SS BOND : bond 0.00447 / 0.28 ( 43) SS BOND : angle 1.66671 / 1.20 ( 86) hydrogen bonds : bond 0.04819 / 3.21 ( 1076) hydrogen bonds : angle 5.14912 / 3.56 ( 2994) link_BETA1-4 : bond 0.00291 / 0.20 ( 18) link_BETA1-4 : angle 1.01610 / 0.67 ( 54) link_NAG-ASN : bond 0.00435 / 0.28 ( 45) link_NAG-ASN : angle 2.77281 / 1.97 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 133 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8014 (ttpp) REVERT: A 878 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8627 (tt) REVERT: A 912 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8795 (p) REVERT: B 117 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8168 (tt) REVERT: C 52 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 58 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.7986 (m-10) REVERT: C 342 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7351 (t80) REVERT: C 495 TYR cc_start: 0.6797 (m-80) cc_final: 0.6407 (m-80) REVERT: C 759 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7565 (t80) REVERT: I 79 MET cc_start: -0.0529 (mpp) cc_final: -0.0733 (mpp) REVERT: I 105 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7346 (tm-30) outliers start: 100 outliers final: 78 residues processed: 222 average time/residue: 0.1658 time to fit residues: 61.1452 Evaluate side-chains 207 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 121 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 13 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 165 optimal weight: 0.3980 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 369 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.159950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109323 restraints weight = 70129.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.109885 restraints weight = 43532.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108981 restraints weight = 32785.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109593 restraints weight = 30654.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110054 restraints weight = 25961.777| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 30669 Z= 0.105 Angle : 0.547 10.774 41893 Z= 0.272 Chirality : 0.044 0.426 4944 Planarity : 0.003 0.051 5287 Dihedral : 3.914 26.332 4030 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 2.62 % Allowed : 17.46 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3709 helix: 2.16 (0.22), residues: 670 sheet: 0.21 (0.17), residues: 949 loop : -1.08 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.021 0.001 TYR B 369 PHE 0.027 0.001 PHE C 377 TRP 0.013 0.001 TRP C 104 HIS 0.001 0.000 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (30563) covalent geometry : angle 0.52496 / 0.27 (41618) SS BOND : bond 0.00480 / 0.28 ( 43) SS BOND : angle 1.31917 / 0.94 ( 86) hydrogen bonds : bond 0.04111 / 2.73 ( 1076) hydrogen bonds : angle 4.94318 / 3.42 ( 2994) link_BETA1-4 : bond 0.00338 / 0.22 ( 18) link_BETA1-4 : angle 0.96613 / 0.64 ( 54) link_NAG-ASN : bond 0.00423 / 0.27 ( 45) link_NAG-ASN : angle 2.54882 / 1.83 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 132 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7522 (m) REVERT: A 733 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7848 (ttpp) REVERT: A 912 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8608 (p) REVERT: B 117 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7924 (tt) REVERT: B 432 CYS cc_start: 0.5049 (OUTLIER) cc_final: 0.3340 (p) REVERT: C 342 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7408 (t80) REVERT: C 495 TYR cc_start: 0.6768 (m-80) cc_final: 0.6434 (m-80) REVERT: C 553 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8530 (p) REVERT: C 759 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7656 (t80) REVERT: C 902 MET cc_start: 0.8730 (tpp) cc_final: 0.8398 (tpt) REVERT: I 79 MET cc_start: -0.0468 (mpp) cc_final: -0.0730 (mpp) REVERT: I 105 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7357 (tm-30) outliers start: 84 outliers final: 61 residues processed: 205 average time/residue: 0.1571 time to fit residues: 53.4975 Evaluate side-chains 195 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 125 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 82 optimal weight: 9.9990 chunk 330 optimal weight: 0.0470 chunk 12 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 302 optimal weight: 0.5980 chunk 344 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 264 optimal weight: 0.5980 chunk 246 optimal weight: 0.0870 chunk 364 optimal weight: 40.0000 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.160966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.110512 restraints weight = 70313.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.111204 restraints weight = 42577.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.110693 restraints weight = 32355.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.111082 restraints weight = 28204.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.111380 restraints weight = 25433.827| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30669 Z= 0.093 Angle : 0.531 10.165 41893 Z= 0.263 Chirality : 0.043 0.375 4944 Planarity : 0.003 0.052 5287 Dihedral : 3.731 26.029 4030 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 2.19 % Allowed : 18.12 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3709 helix: 2.30 (0.22), residues: 667 sheet: 0.28 (0.17), residues: 954 loop : -0.99 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 905 TYR 0.018 0.001 TYR B 904 PHE 0.023 0.001 PHE C 377 TRP 0.013 0.001 TRP C 104 HIS 0.001 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (30563) covalent geometry : angle 0.51115 / 0.26 (41618) SS BOND : bond 0.00371 / 0.23 ( 43) SS BOND : angle 1.14539 / 0.79 ( 86) hydrogen bonds : bond 0.03623 / 2.40 ( 1076) hydrogen bonds : angle 4.76339 / 3.30 ( 2994) link_BETA1-4 : bond 0.00373 / 0.24 ( 18) link_BETA1-4 : angle 0.91853 / 0.61 ( 54) link_NAG-ASN : bond 0.00439 / 0.28 ( 45) link_NAG-ASN : angle 2.42077 / 1.73 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 137 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7501 (m) REVERT: A 1050 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8071 (ptt) REVERT: B 117 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7700 (tt) REVERT: C 342 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7576 (t80) REVERT: C 495 TYR cc_start: 0.6844 (m-80) cc_final: 0.6495 (m-80) REVERT: C 553 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8550 (p) REVERT: C 759 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7646 (t80) REVERT: C 902 MET cc_start: 0.8643 (tpp) cc_final: 0.8242 (tpt) REVERT: I 79 MET cc_start: -0.0684 (mpp) cc_final: -0.0994 (mpp) REVERT: I 105 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7330 (tm-30) outliers start: 70 outliers final: 54 residues processed: 198 average time/residue: 0.1671 time to fit residues: 55.6384 Evaluate side-chains 184 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 123 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 156 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 302 optimal weight: 0.5980 chunk 320 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 312 optimal weight: 40.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.165228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.127729 restraints weight = 76446.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.121787 restraints weight = 55204.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.119733 restraints weight = 49364.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.118824 restraints weight = 39016.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.118886 restraints weight = 36878.005| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30669 Z= 0.103 Angle : 0.544 12.738 41893 Z= 0.267 Chirality : 0.043 0.366 4944 Planarity : 0.003 0.055 5287 Dihedral : 3.697 26.005 4030 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 2.22 % Allowed : 18.09 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3709 helix: 2.31 (0.22), residues: 667 sheet: 0.31 (0.17), residues: 952 loop : -0.97 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.017 0.001 TYR B1067 PHE 0.020 0.001 PHE C 377 TRP 0.011 0.001 TRP B 104 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (30563) covalent geometry : angle 0.52416 / 0.26 (41618) SS BOND : bond 0.00369 / 0.23 ( 43) SS BOND : angle 1.14911 / 0.80 ( 86) hydrogen bonds : bond 0.03668 / 2.43 ( 1076) hydrogen bonds : angle 4.72953 / 3.28 ( 2994) link_BETA1-4 : bond 0.00346 / 0.23 ( 18) link_BETA1-4 : angle 0.92359 / 0.62 ( 54) link_NAG-ASN : bond 0.00415 / 0.26 ( 45) link_NAG-ASN : angle 2.40897 / 1.71 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 125 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7470 (m) REVERT: B 117 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7898 (tt) REVERT: C 342 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7411 (t80) REVERT: C 553 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8699 (p) REVERT: C 759 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7612 (t80) REVERT: C 902 MET cc_start: 0.8823 (tpp) cc_final: 0.8440 (tpt) REVERT: I 79 MET cc_start: -0.0614 (mpp) cc_final: -0.0838 (mpp) REVERT: I 105 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7091 (tm-30) outliers start: 71 outliers final: 57 residues processed: 185 average time/residue: 0.1679 time to fit residues: 52.2970 Evaluate side-chains 185 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 322 optimal weight: 7.9990 chunk 212 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 353 optimal weight: 6.9990 chunk 279 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.158319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.113152 restraints weight = 65160.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108927 restraints weight = 40617.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.109995 restraints weight = 36885.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.109374 restraints weight = 31725.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109847 restraints weight = 28163.014| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.331 30669 Z= 0.151 Angle : 0.693 59.194 41893 Z= 0.368 Chirality : 0.043 0.366 4944 Planarity : 0.003 0.055 5287 Dihedral : 3.704 25.913 4030 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 2.16 % Allowed : 18.24 % Favored : 79.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3709 helix: 2.32 (0.22), residues: 667 sheet: 0.31 (0.17), residues: 952 loop : -0.97 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 328 TYR 0.017 0.001 TYR C1067 PHE 0.016 0.001 PHE A 201 TRP 0.010 0.001 TRP B 104 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (30563) covalent geometry : angle 0.65481 / 0.36 (41618) SS BOND : bond 0.01720 / 1.24 ( 43) SS BOND : angle 4.06505 / 2.89 ( 86) hydrogen bonds : bond 0.03671 / 2.43 ( 1076) hydrogen bonds : angle 4.72710 / 3.28 ( 2994) link_BETA1-4 : bond 0.00345 / 0.23 ( 18) link_BETA1-4 : angle 0.92351 / 0.62 ( 54) link_NAG-ASN : bond 0.00415 / 0.26 ( 45) link_NAG-ASN : angle 2.40905 / 1.71 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4889.34 seconds wall clock time: 85 minutes 21.28 seconds (5121.28 seconds total)