Starting phenix.real_space_refine on Mon Aug 25 10:31:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhy_46892/08_2025/9dhy_46892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhy_46892/08_2025/9dhy_46892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dhy_46892/08_2025/9dhy_46892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhy_46892/08_2025/9dhy_46892.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhy_46892/08_2025/9dhy_46892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhy_46892/08_2025/9dhy_46892.cif" } resolution = 2.7 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= 0.014 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 117 5.16 5 C 17319 2.51 5 N 4491 2.21 5 O 5300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 246 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27227 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7122 Classifications: {'peptide': 912} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 864} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 7138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7138 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 866} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "J" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 7138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7138 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 866} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.26, per 1000 atoms: 0.27 Number of scatterers: 27227 At special positions: 0 Unit cell: (155.43, 152.46, 167.31, 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 117 16.00 O 5300 8.00 N 4491 7.00 C 17319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.02 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.02 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.02 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.03 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.03 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.02 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.03 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.03 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.03 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.02 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 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-ASN " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C 331 " " NAG F1301 " - " ASN F 282 " " NAG F1302 " - " ASN F 343 " " NAG F1303 " - " ASN F 616 " " NAG F1304 " - " ASN F 709 " " NAG F1305 " - " ASN F1074 " " NAG F1306 " - " ASN F1098 " " NAG F1307 " - " ASN F 331 " " NAG G 1 " - " ASN C 801 " " NAG H 1 " - " ASN C1134 " " NAG K1301 " - " ASN K 282 " " NAG K1302 " - " ASN K 343 " " NAG K1303 " - " ASN K 616 " " NAG K1304 " - " ASN K 709 " " NAG K1305 " - " ASN K1074 " " NAG K1306 " - " ASN K1098 " " NAG K1307 " - " ASN K 331 " " NAG L 1 " - " ASN F 801 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN F 717 " " NAG O 1 " - " ASN F1134 " " NAG P 1 " - " ASN K 717 " " NAG Q 1 " - " ASN K 801 " " NAG R 1 " - " ASN K1134 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6362 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 23.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.947A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.780A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.614A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.031A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.256A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 411' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.017A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (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 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.234A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.880A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.628A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.502A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.059A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.213A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.947A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 337 through 343 removed outlier: 3.780A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 371 removed outlier: 4.615A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 388 removed outlier: 4.031A pdb=" N ASN F 388 " --> pdb=" O PRO F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.256A pdb=" N GLN F 409 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE F 410 " --> pdb=" O GLU F 406 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA F 411 " --> pdb=" O VAL F 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 405 through 411' Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 757 through 783 removed outlier: 4.017A pdb=" N THR F 761 " --> pdb=" O GLY F 757 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 897 through 910 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.234A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 removed outlier: 3.880A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) Processing helix chain 'F' and resid 942 through 944 No H-bonds generated for 'chain 'F' and resid 942 through 944' Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.627A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 removed outlier: 3.503A pdb=" N ILE F 980 " --> pdb=" O VAL F 976 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 1032 removed outlier: 4.059A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1145 removed outlier: 4.213A pdb=" N GLU F1144 " --> pdb=" O PRO F1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.947A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'K' and resid 294 through 304 Processing helix chain 'K' and resid 337 through 343 removed outlier: 3.780A pdb=" N VAL K 341 " --> pdb=" O PRO K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 371 removed outlier: 4.614A pdb=" N LEU K 368 " --> pdb=" O ASP K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 388 removed outlier: 4.031A pdb=" N ASN K 388 " --> pdb=" O PRO K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 411 removed outlier: 4.256A pdb=" N GLN K 409 " --> pdb=" O ASP K 405 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE K 410 " --> pdb=" O GLU K 406 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA K 411 " --> pdb=" O VAL K 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 405 through 411' Processing helix chain 'K' and resid 416 through 421 Processing helix chain 'K' and resid 438 through 443 Processing helix chain 'K' and resid 737 through 743 Processing helix chain 'K' and resid 746 through 754 Processing helix chain 'K' and resid 757 through 783 removed outlier: 4.017A pdb=" N THR K 761 " --> pdb=" O GLY K 757 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 826 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 897 through 910 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.234A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 941 removed outlier: 3.880A pdb=" N GLN K 935 " --> pdb=" O ILE K 931 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP K 936 " --> pdb=" O GLY K 932 " (cutoff:3.500A) Processing helix chain 'K' and resid 942 through 944 No H-bonds generated for 'chain 'K' and resid 942 through 944' Processing helix chain 'K' and resid 945 through 965 removed outlier: 3.627A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 984 removed outlier: 3.503A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 985 through 1032 removed outlier: 4.059A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) Processing helix chain 'K' and resid 1140 through 1145 removed outlier: 4.212A pdb=" N GLU K1144 " --> pdb=" O PRO K1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.750A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.531A pdb=" N VAL A 112 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.669A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 29 through 30 removed outlier: 8.898A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.845A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.007A pdb=" N ILE C 128 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL C 171 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.827A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.016A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.516A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.078A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.885A pdb=" N ALA C 701 " --> pdb=" O ILE F 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.626A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.626A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.533A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'C' and resid 1120 through 1124 removed outlier: 6.559A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.750A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.509A pdb=" N VAL D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.669A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 29 through 30 removed outlier: 8.898A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU F 224 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS F 207 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N ALA F 222 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL F 36 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 48 through 51 removed outlier: 3.845A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 84 through 85 removed outlier: 5.006A pdb=" N ILE F 128 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL F 171 " --> pdb=" O ILE F 128 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 311 through 319 removed outlier: 6.827A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN F 317 " --> pdb=" O GLY F 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY F 593 " --> pdb=" O ASN F 317 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 325 through 328 removed outlier: 6.017A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.517A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN F 437 " --> pdb=" O PHE F 374 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE F 374 " --> pdb=" O ASN F 437 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.077A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 701 through 702 removed outlier: 6.863A pdb=" N ALA F 701 " --> pdb=" O ILE K 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.626A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE F 720 " --> pdb=" O TYR F1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR F1067 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL F 722 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL F1065 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR F 724 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU F1063 " --> pdb=" O THR F 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 726 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL F1061 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY F1059 " --> pdb=" O PRO F 728 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.626A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE F 720 " --> pdb=" O TYR F1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR F1067 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL F 722 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL F1065 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR F 724 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU F1063 " --> pdb=" O THR F 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 726 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL F1061 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY F1059 " --> pdb=" O PRO F 728 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F1076 " --> pdb=" O SER F1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.532A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 1120 through 1124 removed outlier: 6.559A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.749A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.516A pdb=" N VAL I 112 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.668A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 29 through 30 removed outlier: 8.899A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU K 224 " --> pdb=" O SER K 205 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS K 207 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ALA K 222 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL K 36 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 48 through 51 removed outlier: 3.844A pdb=" N ASP K 287 " --> pdb=" O LYS K 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 84 through 85 removed outlier: 5.008A pdb=" N ILE K 128 " --> pdb=" O VAL K 171 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL K 171 " --> pdb=" O ILE K 128 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 311 through 319 removed outlier: 6.827A pdb=" N VAL K 595 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN K 317 " --> pdb=" O GLY K 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY K 593 " --> pdb=" O ASN K 317 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 325 through 328 removed outlier: 6.017A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 354 through 358 removed outlier: 3.517A pdb=" N ASN K 354 " --> pdb=" O SER K 399 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN K 437 " --> pdb=" O PHE K 374 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE K 374 " --> pdb=" O ASN K 437 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.078A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.626A pdb=" N GLN K1071 " --> pdb=" O THR K 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE K 718 " --> pdb=" O PRO K1069 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE K 720 " --> pdb=" O TYR K1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR K1067 " --> pdb=" O ILE K 720 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL K 722 " --> pdb=" O VAL K1065 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL K1065 " --> pdb=" O VAL K 722 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR K 724 " --> pdb=" O LEU K1063 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU K1063 " --> pdb=" O THR K 724 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE K 726 " --> pdb=" O VAL K1061 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL K1061 " --> pdb=" O ILE K 726 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY K1059 " --> pdb=" O PRO K 728 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.626A pdb=" N GLN K1071 " --> pdb=" O THR K 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE K 718 " --> pdb=" O PRO K1069 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE K 720 " --> pdb=" O TYR K1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR K1067 " --> pdb=" O ILE K 720 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL K 722 " --> pdb=" O VAL K1065 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL K1065 " --> pdb=" O VAL K 722 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR K 724 " --> pdb=" O LEU K1063 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU K1063 " --> pdb=" O THR K 724 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE K 726 " --> pdb=" O VAL K1061 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL K1061 " --> pdb=" O ILE K 726 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY K1059 " --> pdb=" O PRO K 728 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR K1076 " --> pdb=" O SER K1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA K1078 " --> pdb=" O PHE K1095 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.533A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 1120 through 1124 removed outlier: 6.560A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.34 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7454 1.33 - 1.45: 5318 1.45 - 1.57: 14887 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 27809 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" C1 NAG F1307 " pdb=" O5 NAG F1307 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.76e+00 bond pdb=" C1 NAG K1307 " pdb=" O5 NAG K1307 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.352 0.054 2.00e-02 2.50e+03 7.26e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.353 0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 27804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 34733 1.80 - 3.60: 2635 3.60 - 5.40: 367 5.40 - 7.20: 64 7.20 - 9.00: 6 Bond angle restraints: 37805 Sorted by residual: angle pdb=" N PRO K 892 " pdb=" CA PRO K 892 " pdb=" CB PRO K 892 " ideal model delta sigma weight residual 103.27 109.41 -6.14 9.00e-01 1.23e+00 4.65e+01 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.27 109.40 -6.13 9.00e-01 1.23e+00 4.64e+01 angle pdb=" N PRO F 892 " pdb=" CA PRO F 892 " pdb=" CB PRO F 892 " ideal model delta sigma weight residual 103.27 109.36 -6.09 9.00e-01 1.23e+00 4.58e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" CB PRO C 942 " ideal model delta sigma weight residual 103.44 110.06 -6.62 1.12e+00 7.97e-01 3.49e+01 angle pdb=" N PRO F 942 " pdb=" CA PRO F 942 " pdb=" CB PRO F 942 " ideal model delta sigma weight residual 103.44 110.04 -6.60 1.12e+00 7.97e-01 3.47e+01 ... (remaining 37800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 16043 17.74 - 35.49: 812 35.49 - 53.23: 125 53.23 - 70.97: 31 70.97 - 88.72: 3 Dihedral angle restraints: 17014 sinusoidal: 7114 harmonic: 9900 Sorted by residual: dihedral pdb=" CB CYS F 538 " pdb=" SG CYS F 538 " pdb=" SG CYS F 590 " pdb=" CB CYS F 590 " ideal model delta sinusoidal sigma weight residual -86.00 -144.74 58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -144.74 58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS K 538 " pdb=" SG CYS K 538 " pdb=" SG CYS K 590 " pdb=" CB CYS K 590 " ideal model delta sinusoidal sigma weight residual -86.00 -144.73 58.73 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 17011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 4356 0.166 - 0.332: 63 0.332 - 0.498: 0 0.498 - 0.663: 0 0.663 - 0.829: 3 Chirality restraints: 4422 Sorted by residual: chirality pdb=" C1 NAG F1307 " pdb=" ND2 ASN F 331 " pdb=" C2 NAG F1307 " pdb=" O5 NAG F1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG K1307 " pdb=" ND2 ASN K 331 " pdb=" C2 NAG K1307 " pdb=" O5 NAG K1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 4419 not shown) Planarity restraints: 4836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 789 " 0.006 2.00e-02 2.50e+03 2.07e-02 8.60e+00 pdb=" CG TYR K 789 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR K 789 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR K 789 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR K 789 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR K 789 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR K 789 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR K 789 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 789 " -0.007 2.00e-02 2.50e+03 2.06e-02 8.52e+00 pdb=" CG TYR F 789 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 789 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 789 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR F 789 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 789 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR F 789 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 789 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 789 " -0.007 2.00e-02 2.50e+03 2.05e-02 8.40e+00 pdb=" CG TYR C 789 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR C 789 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 789 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR C 789 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 789 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 789 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 789 " 0.011 2.00e-02 2.50e+03 ... (remaining 4833 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4854 2.76 - 3.29: 25075 3.29 - 3.83: 45082 3.83 - 4.36: 54268 4.36 - 4.90: 93715 Nonbonded interactions: 222994 Sorted by model distance: nonbonded pdb=" OE2 GLU F 702 " pdb=" ND2 ASN J 31 " model vdw 2.223 3.120 nonbonded pdb=" OE2 GLU C 702 " pdb=" ND2 ASN E 31 " model vdw 2.224 3.120 nonbonded pdb=" ND2 ASN B 31 " pdb=" OE2 GLU K 702 " model vdw 2.228 3.120 nonbonded pdb=" OG1 THR K 716 " pdb=" O GLN K1071 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR F 716 " pdb=" O GLN F1071 " model vdw 2.334 3.040 ... (remaining 222989 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' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'C' selection = (chain 'F' and (resid 28 through 107 or resid 116 through 1307)) selection = (chain 'K' and (resid 28 through 107 or resid 116 through 1307)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 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: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.290 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.014 0.094 27890 Z= 0.573 Angle : 1.059 18.831 38006 Z= 0.617 Chirality : 0.069 0.829 4422 Planarity : 0.005 0.028 4806 Dihedral : 10.273 88.719 10526 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.05 % Allowed : 4.20 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.14), residues: 3343 helix: 1.47 (0.19), residues: 618 sheet: 2.02 (0.17), residues: 865 loop : -0.18 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F1039 TYR 0.048 0.003 TYR K 789 PHE 0.033 0.004 PHE K 543 TRP 0.022 0.003 TRP K 104 HIS 0.018 0.004 HIS F1064 Details of bonding type rmsd covalent geometry : bond 0.01362 (27809) covalent geometry : angle 1.03137 (37805) SS BOND : bond 0.00538 ( 42) SS BOND : angle 1.19784 ( 84) hydrogen bonds : bond 0.20165 ( 1138) hydrogen bonds : angle 8.46997 ( 3162) link_BETA1-4 : bond 0.00391 ( 9) link_BETA1-4 : angle 3.11499 ( 27) link_NAG-ASN : bond 0.00853 ( 30) link_NAG-ASN : angle 4.77775 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 493 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8653 (m-30) cc_final: 0.8332 (m-30) REVERT: C 314 GLN cc_start: 0.8504 (tt0) cc_final: 0.7988 (tm-30) REVERT: C 360 ASN cc_start: 0.8912 (t0) cc_final: 0.8400 (t0) REVERT: C 392 PHE cc_start: 0.8326 (m-80) cc_final: 0.8124 (m-80) REVERT: C 400 PHE cc_start: 0.8836 (p90) cc_final: 0.8407 (p90) REVERT: C 512 VAL cc_start: 0.8626 (t) cc_final: 0.8318 (m) REVERT: C 516 GLU cc_start: 0.8080 (tt0) cc_final: 0.7777 (mt-10) REVERT: C 533 LEU cc_start: 0.9037 (tp) cc_final: 0.8734 (mt) REVERT: C 559 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7934 (t80) REVERT: C 565 PHE cc_start: 0.7996 (m-80) cc_final: 0.7794 (m-10) REVERT: C 645 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8695 (p) REVERT: C 988 GLU cc_start: 0.7931 (mp0) cc_final: 0.7623 (mp0) REVERT: C 1029 MET cc_start: 0.9193 (tpp) cc_final: 0.8962 (tpp) REVERT: C 1100 THR cc_start: 0.8775 (p) cc_final: 0.8558 (t) REVERT: D 31 ASP cc_start: 0.8635 (m-30) cc_final: 0.8385 (m-30) REVERT: D 111 ASP cc_start: 0.8351 (t0) cc_final: 0.8079 (t0) REVERT: F 200 TYR cc_start: 0.8101 (m-80) cc_final: 0.7875 (m-10) REVERT: F 265 TYR cc_start: 0.6763 (p90) cc_final: 0.5903 (p90) REVERT: F 269 TYR cc_start: 0.7922 (m-80) cc_final: 0.7602 (m-80) REVERT: F 360 ASN cc_start: 0.9025 (t0) cc_final: 0.8551 (t0) REVERT: F 392 PHE cc_start: 0.8262 (m-80) cc_final: 0.8011 (m-80) REVERT: F 400 PHE cc_start: 0.8779 (p90) cc_final: 0.8451 (p90) REVERT: F 512 VAL cc_start: 0.8561 (t) cc_final: 0.8248 (m) REVERT: F 516 GLU cc_start: 0.8089 (tt0) cc_final: 0.7721 (mt-10) REVERT: F 533 LEU cc_start: 0.9100 (tp) cc_final: 0.8771 (mt) REVERT: F 565 PHE cc_start: 0.7886 (m-80) cc_final: 0.7616 (m-10) REVERT: F 645 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8649 (p) REVERT: F 1050 MET cc_start: 0.9217 (ptm) cc_final: 0.8991 (ptm) REVERT: F 1100 THR cc_start: 0.8800 (p) cc_final: 0.8553 (t) REVERT: I 31 ASP cc_start: 0.8692 (m-30) cc_final: 0.8412 (m-30) REVERT: I 111 ASP cc_start: 0.8336 (t0) cc_final: 0.8000 (t0) REVERT: J 13 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8581 (p) REVERT: K 200 TYR cc_start: 0.8188 (m-80) cc_final: 0.7969 (m-10) REVERT: K 314 GLN cc_start: 0.8518 (tt0) cc_final: 0.7874 (tm-30) REVERT: K 357 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.7944 (ttp80) REVERT: K 360 ASN cc_start: 0.9105 (t0) cc_final: 0.8580 (t0) REVERT: K 396 TYR cc_start: 0.7303 (m-80) cc_final: 0.6640 (m-10) REVERT: K 400 PHE cc_start: 0.8764 (p90) cc_final: 0.8438 (p90) REVERT: K 512 VAL cc_start: 0.8359 (t) cc_final: 0.8051 (m) REVERT: K 516 GLU cc_start: 0.8105 (tt0) cc_final: 0.7463 (mt-10) REVERT: K 533 LEU cc_start: 0.9055 (tp) cc_final: 0.8702 (mt) REVERT: K 543 PHE cc_start: 0.7475 (m-10) cc_final: 0.7196 (m-10) REVERT: K 645 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8612 (p) outliers start: 61 outliers final: 19 residues processed: 551 average time/residue: 0.6607 time to fit residues: 425.4530 Evaluate side-chains 313 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 645 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 218 GLN C 271 GLN C 613 GLN C 762 GLN C 955 ASN F 87 ASN F 218 GLN F 613 GLN F 762 GLN K 218 GLN K 613 GLN K 762 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.115293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067355 restraints weight = 55573.819| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.68 r_work: 0.2867 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27890 Z= 0.164 Angle : 0.657 12.222 38006 Z= 0.340 Chirality : 0.046 0.221 4422 Planarity : 0.004 0.030 4806 Dihedral : 5.778 58.449 4523 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.56 % Allowed : 11.07 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.14), residues: 3343 helix: 2.89 (0.20), residues: 631 sheet: 1.79 (0.17), residues: 809 loop : -0.16 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 408 TYR 0.033 0.002 TYR K 265 PHE 0.018 0.002 PHE F 58 TRP 0.030 0.002 TRP K 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00374 (27809) covalent geometry : angle 0.63485 (37805) SS BOND : bond 0.00561 ( 42) SS BOND : angle 2.56931 ( 84) hydrogen bonds : bond 0.05967 ( 1138) hydrogen bonds : angle 6.02822 ( 3162) link_BETA1-4 : bond 0.00553 ( 9) link_BETA1-4 : angle 1.65502 ( 27) link_NAG-ASN : bond 0.00402 ( 30) link_NAG-ASN : angle 2.39944 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 343 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8650 (tppp) cc_final: 0.8417 (tppp) REVERT: C 64 TRP cc_start: 0.7717 (t-100) cc_final: 0.7495 (t60) REVERT: C 87 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.6806 (p0) REVERT: C 201 PHE cc_start: 0.8349 (t80) cc_final: 0.8137 (t80) REVERT: C 314 GLN cc_start: 0.8701 (tt0) cc_final: 0.8288 (tm-30) REVERT: C 360 ASN cc_start: 0.8700 (t0) cc_final: 0.8485 (t0) REVERT: C 377 PHE cc_start: 0.8541 (t80) cc_final: 0.8266 (t80) REVERT: C 378 LYS cc_start: 0.8721 (ptpp) cc_final: 0.8465 (ptpp) REVERT: C 421 TYR cc_start: 0.7050 (m-80) cc_final: 0.6336 (m-10) REVERT: C 512 VAL cc_start: 0.8458 (t) cc_final: 0.8119 (m) REVERT: C 533 LEU cc_start: 0.8951 (tp) cc_final: 0.8629 (mt) REVERT: C 559 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7844 (t80) REVERT: C 979 ASP cc_start: 0.8373 (t70) cc_final: 0.7970 (t0) REVERT: C 988 GLU cc_start: 0.8620 (mp0) cc_final: 0.8295 (mp0) REVERT: C 1029 MET cc_start: 0.9529 (tpp) cc_final: 0.9228 (tpp) REVERT: D 82 GLN cc_start: 0.8301 (tp40) cc_final: 0.7917 (tp40) REVERT: F 87 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6847 (p0) REVERT: F 200 TYR cc_start: 0.8464 (m-80) cc_final: 0.8196 (m-10) REVERT: F 201 PHE cc_start: 0.8216 (t80) cc_final: 0.7995 (t80) REVERT: F 265 TYR cc_start: 0.6378 (p90) cc_final: 0.5697 (p90) REVERT: F 314 GLN cc_start: 0.8933 (tt0) cc_final: 0.8469 (tm-30) REVERT: F 360 ASN cc_start: 0.8808 (t0) cc_final: 0.8572 (t0) REVERT: F 374 PHE cc_start: 0.8561 (m-80) cc_final: 0.8320 (m-80) REVERT: F 378 LYS cc_start: 0.8940 (ptpp) cc_final: 0.8722 (ptmm) REVERT: F 400 PHE cc_start: 0.8684 (p90) cc_final: 0.8476 (p90) REVERT: F 512 VAL cc_start: 0.8420 (t) cc_final: 0.8139 (m) REVERT: F 516 GLU cc_start: 0.7795 (tt0) cc_final: 0.7498 (mt-10) REVERT: F 533 LEU cc_start: 0.9023 (tp) cc_final: 0.8703 (mt) REVERT: F 988 GLU cc_start: 0.8472 (mp0) cc_final: 0.8148 (mp0) REVERT: I 30 ASP cc_start: 0.8890 (p0) cc_final: 0.8615 (p0) REVERT: I 32 TYR cc_start: 0.9185 (m-80) cc_final: 0.8966 (m-80) REVERT: I 82 GLN cc_start: 0.8320 (tp40) cc_final: 0.8112 (tp40) REVERT: I 89 GLU cc_start: 0.8584 (pm20) cc_final: 0.8265 (pm20) REVERT: K 200 TYR cc_start: 0.8521 (m-80) cc_final: 0.8307 (m-80) REVERT: K 314 GLN cc_start: 0.8766 (tt0) cc_final: 0.8240 (tm-30) REVERT: K 357 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.8013 (ttp80) REVERT: K 360 ASN cc_start: 0.8990 (t0) cc_final: 0.8561 (t0) REVERT: K 377 PHE cc_start: 0.8390 (t80) cc_final: 0.7962 (t80) REVERT: K 378 LYS cc_start: 0.8818 (ptpp) cc_final: 0.8367 (ptmm) REVERT: K 512 VAL cc_start: 0.8335 (t) cc_final: 0.8038 (m) REVERT: K 516 GLU cc_start: 0.7861 (tt0) cc_final: 0.7471 (mt-10) REVERT: K 533 LEU cc_start: 0.9076 (tp) cc_final: 0.8659 (mt) outliers start: 76 outliers final: 26 residues processed: 400 average time/residue: 0.6430 time to fit residues: 302.0321 Evaluate side-chains 293 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 265 TYR Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 776 LYS Chi-restraints excluded: chain K residue 900 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 323 optimal weight: 0.8980 chunk 318 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN C 87 ASN C 271 GLN F 87 ASN F 437 ASN ** F 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** K 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.114894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067036 restraints weight = 55864.499| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.66 r_work: 0.2843 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27890 Z= 0.148 Angle : 0.593 11.976 38006 Z= 0.306 Chirality : 0.045 0.183 4422 Planarity : 0.004 0.041 4806 Dihedral : 5.317 58.359 4493 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.59 % Allowed : 12.45 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.14), residues: 3343 helix: 2.99 (0.20), residues: 632 sheet: 1.49 (0.17), residues: 818 loop : -0.21 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 18 TYR 0.063 0.001 TYR K 265 PHE 0.019 0.002 PHE K 400 TRP 0.027 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00343 (27809) covalent geometry : angle 0.57959 (37805) SS BOND : bond 0.00460 ( 42) SS BOND : angle 1.42355 ( 84) hydrogen bonds : bond 0.05281 ( 1138) hydrogen bonds : angle 5.56460 ( 3162) link_BETA1-4 : bond 0.00445 ( 9) link_BETA1-4 : angle 1.59088 ( 27) link_NAG-ASN : bond 0.00284 ( 30) link_NAG-ASN : angle 2.12560 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 297 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9034 (p0) cc_final: 0.8799 (p0) REVERT: C 170 TYR cc_start: 0.7680 (t80) cc_final: 0.7309 (t80) REVERT: C 201 PHE cc_start: 0.8383 (t80) cc_final: 0.8047 (t80) REVERT: C 314 GLN cc_start: 0.8775 (tt0) cc_final: 0.8397 (tm-30) REVERT: C 360 ASN cc_start: 0.8694 (t0) cc_final: 0.8218 (t0) REVERT: C 377 PHE cc_start: 0.8618 (t80) cc_final: 0.8410 (t80) REVERT: C 421 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6470 (m-80) REVERT: C 512 VAL cc_start: 0.8466 (t) cc_final: 0.8198 (m) REVERT: C 533 LEU cc_start: 0.8939 (tp) cc_final: 0.8627 (mt) REVERT: C 559 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7862 (t80) REVERT: C 979 ASP cc_start: 0.8405 (t70) cc_final: 0.7996 (t0) REVERT: C 1029 MET cc_start: 0.9517 (tpp) cc_final: 0.9232 (tpp) REVERT: D 82 GLN cc_start: 0.8373 (tp40) cc_final: 0.7662 (tp40) REVERT: F 170 TYR cc_start: 0.7526 (t80) cc_final: 0.7132 (t80) REVERT: F 200 TYR cc_start: 0.8399 (m-80) cc_final: 0.8108 (m-10) REVERT: F 201 PHE cc_start: 0.8222 (t80) cc_final: 0.7798 (t80) REVERT: F 265 TYR cc_start: 0.6373 (p90) cc_final: 0.5749 (p90) REVERT: F 310 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8476 (ttmm) REVERT: F 314 GLN cc_start: 0.8994 (tt0) cc_final: 0.8564 (tm-30) REVERT: F 360 ASN cc_start: 0.8889 (t0) cc_final: 0.8471 (t0) REVERT: F 378 LYS cc_start: 0.8914 (ptpp) cc_final: 0.8708 (ptmm) REVERT: F 512 VAL cc_start: 0.8451 (t) cc_final: 0.8225 (m) REVERT: F 533 LEU cc_start: 0.9027 (tp) cc_final: 0.8710 (mt) REVERT: F 564 GLN cc_start: 0.7970 (mt0) cc_final: 0.7764 (mt0) REVERT: F 988 GLU cc_start: 0.8480 (mp0) cc_final: 0.8130 (mp0) REVERT: I 30 ASP cc_start: 0.8983 (p0) cc_final: 0.8721 (p0) REVERT: I 32 TYR cc_start: 0.9193 (m-80) cc_final: 0.8941 (m-80) REVERT: I 87 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7548 (mtt-85) REVERT: I 89 GLU cc_start: 0.8575 (pm20) cc_final: 0.8172 (pm20) REVERT: K 200 TYR cc_start: 0.8572 (m-80) cc_final: 0.8358 (m-10) REVERT: K 314 GLN cc_start: 0.8802 (tt0) cc_final: 0.8353 (tm-30) REVERT: K 360 ASN cc_start: 0.8810 (t0) cc_final: 0.8524 (t0) REVERT: K 377 PHE cc_start: 0.8609 (t80) cc_final: 0.8288 (t80) REVERT: K 396 TYR cc_start: 0.7208 (m-10) cc_final: 0.6576 (m-80) REVERT: K 434 ILE cc_start: 0.8558 (mt) cc_final: 0.8357 (mm) REVERT: K 512 VAL cc_start: 0.8373 (t) cc_final: 0.8159 (m) REVERT: K 516 GLU cc_start: 0.7657 (tt0) cc_final: 0.7419 (mt-10) REVERT: K 533 LEU cc_start: 0.9044 (tp) cc_final: 0.8650 (mt) outliers start: 77 outliers final: 28 residues processed: 358 average time/residue: 0.6627 time to fit residues: 277.6426 Evaluate side-chains 294 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 310 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 916 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 36 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 247 optimal weight: 0.3980 chunk 126 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 335 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 965 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 = 0.3870 r_free = 0.3870 target = 0.115730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068424 restraints weight = 55404.888| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.64 r_work: 0.2875 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27890 Z= 0.114 Angle : 0.544 8.961 38006 Z= 0.280 Chirality : 0.043 0.162 4422 Planarity : 0.004 0.039 4806 Dihedral : 5.061 57.570 4493 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.59 % Allowed : 12.65 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.14), residues: 3343 helix: 3.10 (0.20), residues: 635 sheet: 1.26 (0.16), residues: 842 loop : -0.22 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 18 TYR 0.030 0.001 TYR C 265 PHE 0.019 0.001 PHE K 400 TRP 0.033 0.001 TRP C 436 HIS 0.004 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00252 (27809) covalent geometry : angle 0.53361 (37805) SS BOND : bond 0.00539 ( 42) SS BOND : angle 1.32281 ( 84) hydrogen bonds : bond 0.04515 ( 1138) hydrogen bonds : angle 5.21743 ( 3162) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 1.46638 ( 27) link_NAG-ASN : bond 0.00341 ( 30) link_NAG-ASN : angle 1.77173 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 300 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9041 (p0) cc_final: 0.8740 (p0) REVERT: B 82 ASP cc_start: 0.8239 (m-30) cc_final: 0.7957 (m-30) REVERT: C 170 TYR cc_start: 0.7769 (t80) cc_final: 0.7356 (t80) REVERT: C 201 PHE cc_start: 0.8362 (t80) cc_final: 0.8147 (t80) REVERT: C 314 GLN cc_start: 0.8800 (tt0) cc_final: 0.8427 (tm-30) REVERT: C 512 VAL cc_start: 0.8423 (t) cc_final: 0.8173 (m) REVERT: C 533 LEU cc_start: 0.8936 (tp) cc_final: 0.8651 (mt) REVERT: C 559 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7978 (t80) REVERT: C 900 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8825 (mtm) REVERT: C 979 ASP cc_start: 0.8413 (t70) cc_final: 0.8015 (t0) REVERT: C 1029 MET cc_start: 0.9509 (tpp) cc_final: 0.9121 (tpp) REVERT: C 1050 MET cc_start: 0.9044 (ptm) cc_final: 0.8833 (ptm) REVERT: D 82 GLN cc_start: 0.8426 (tp40) cc_final: 0.7708 (tp40) REVERT: D 89 GLU cc_start: 0.8543 (pm20) cc_final: 0.8242 (pm20) REVERT: F 170 TYR cc_start: 0.7756 (t80) cc_final: 0.7278 (t80) REVERT: F 200 TYR cc_start: 0.8394 (m-80) cc_final: 0.8140 (m-10) REVERT: F 201 PHE cc_start: 0.8197 (t80) cc_final: 0.7949 (t80) REVERT: F 265 TYR cc_start: 0.6206 (p90) cc_final: 0.5560 (p90) REVERT: F 314 GLN cc_start: 0.8998 (tt0) cc_final: 0.8646 (tm-30) REVERT: F 378 LYS cc_start: 0.8951 (ptpp) cc_final: 0.8722 (ptmm) REVERT: F 512 VAL cc_start: 0.8463 (t) cc_final: 0.8193 (m) REVERT: F 533 LEU cc_start: 0.9030 (tp) cc_final: 0.8731 (mt) REVERT: F 559 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7800 (t80) REVERT: F 979 ASP cc_start: 0.8608 (t0) cc_final: 0.8399 (OUTLIER) REVERT: F 988 GLU cc_start: 0.8562 (mp0) cc_final: 0.8337 (mp0) REVERT: I 30 ASP cc_start: 0.9013 (p0) cc_final: 0.8720 (p0) REVERT: I 73 ASP cc_start: 0.7958 (t0) cc_final: 0.7129 (t0) REVERT: I 87 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7685 (mtt-85) REVERT: J 105 GLU cc_start: 0.4467 (tm-30) cc_final: 0.4145 (tm-30) REVERT: K 170 TYR cc_start: 0.7583 (t80) cc_final: 0.7218 (t80) REVERT: K 200 TYR cc_start: 0.8633 (m-80) cc_final: 0.8270 (m-10) REVERT: K 314 GLN cc_start: 0.8833 (tt0) cc_final: 0.8399 (tm-30) REVERT: K 377 PHE cc_start: 0.8653 (t80) cc_final: 0.8241 (t80) REVERT: K 512 VAL cc_start: 0.8423 (t) cc_final: 0.8214 (m) REVERT: K 533 LEU cc_start: 0.9026 (tp) cc_final: 0.8669 (mt) REVERT: K 559 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7978 (t80) outliers start: 77 outliers final: 31 residues processed: 359 average time/residue: 0.6053 time to fit residues: 256.8812 Evaluate side-chains 299 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 559 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 41 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 262 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN E 37 GLN F 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.113792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065951 restraints weight = 55309.487| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.62 r_work: 0.2822 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27890 Z= 0.185 Angle : 0.582 10.679 38006 Z= 0.299 Chirality : 0.045 0.167 4422 Planarity : 0.004 0.045 4806 Dihedral : 5.132 59.369 4493 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.42 % Allowed : 13.35 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.14), residues: 3343 helix: 2.92 (0.20), residues: 636 sheet: 1.09 (0.16), residues: 919 loop : -0.32 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 87 TYR 0.030 0.001 TYR K 756 PHE 0.021 0.002 PHE C 377 TRP 0.034 0.001 TRP K 436 HIS 0.008 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00444 (27809) covalent geometry : angle 0.57008 (37805) SS BOND : bond 0.00541 ( 42) SS BOND : angle 1.38078 ( 84) hydrogen bonds : bond 0.05145 ( 1138) hydrogen bonds : angle 5.25365 ( 3162) link_BETA1-4 : bond 0.00312 ( 9) link_BETA1-4 : angle 1.60535 ( 27) link_NAG-ASN : bond 0.00179 ( 30) link_NAG-ASN : angle 1.96935 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 277 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9078 (p0) cc_final: 0.8849 (p0) REVERT: A 73 ASP cc_start: 0.8092 (t0) cc_final: 0.7405 (t0) REVERT: C 170 TYR cc_start: 0.7937 (t80) cc_final: 0.7571 (t80) REVERT: C 314 GLN cc_start: 0.8962 (tt0) cc_final: 0.8558 (tm-30) REVERT: C 377 PHE cc_start: 0.8588 (t80) cc_final: 0.8351 (t80) REVERT: C 512 VAL cc_start: 0.8447 (t) cc_final: 0.8183 (m) REVERT: C 533 LEU cc_start: 0.8964 (tp) cc_final: 0.8639 (mt) REVERT: C 559 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.8059 (t80) REVERT: C 581 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8663 (p) REVERT: C 979 ASP cc_start: 0.8411 (t70) cc_final: 0.8105 (t0) REVERT: C 1029 MET cc_start: 0.9520 (tpp) cc_final: 0.9167 (tpp) REVERT: D 73 ASP cc_start: 0.8123 (t0) cc_final: 0.7254 (t0) REVERT: D 76 LYS cc_start: 0.9274 (mttp) cc_final: 0.8894 (ttmm) REVERT: D 82 GLN cc_start: 0.8437 (tp40) cc_final: 0.7675 (tp40) REVERT: D 89 GLU cc_start: 0.8515 (pm20) cc_final: 0.8303 (pm20) REVERT: F 64 TRP cc_start: 0.7696 (t60) cc_final: 0.7456 (t60) REVERT: F 200 TYR cc_start: 0.8456 (m-80) cc_final: 0.8163 (m-10) REVERT: F 201 PHE cc_start: 0.8331 (t80) cc_final: 0.7901 (t80) REVERT: F 265 TYR cc_start: 0.6268 (p90) cc_final: 0.5619 (p90) REVERT: F 314 GLN cc_start: 0.9029 (tt0) cc_final: 0.8642 (tm-30) REVERT: F 378 LYS cc_start: 0.8962 (ptpp) cc_final: 0.8674 (ptmm) REVERT: F 512 VAL cc_start: 0.8470 (t) cc_final: 0.8207 (m) REVERT: F 533 LEU cc_start: 0.9047 (tp) cc_final: 0.8731 (mt) REVERT: F 559 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7884 (t80) REVERT: F 581 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8726 (p) REVERT: F 979 ASP cc_start: 0.8618 (t0) cc_final: 0.8399 (t0) REVERT: F 988 GLU cc_start: 0.8561 (mp0) cc_final: 0.8314 (mp0) REVERT: I 30 ASP cc_start: 0.9028 (p0) cc_final: 0.8792 (p0) REVERT: I 73 ASP cc_start: 0.8116 (t0) cc_final: 0.7321 (t0) REVERT: J 24 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7688 (mtp-110) REVERT: K 170 TYR cc_start: 0.7755 (t80) cc_final: 0.7468 (t80) REVERT: K 200 TYR cc_start: 0.8580 (m-80) cc_final: 0.8205 (m-10) REVERT: K 314 GLN cc_start: 0.8901 (tt0) cc_final: 0.8450 (tm-30) REVERT: K 512 VAL cc_start: 0.8437 (t) cc_final: 0.8190 (m) REVERT: K 533 LEU cc_start: 0.9039 (tp) cc_final: 0.8656 (mt) REVERT: K 559 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7971 (t80) REVERT: K 581 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8655 (p) outliers start: 72 outliers final: 42 residues processed: 333 average time/residue: 0.5590 time to fit residues: 220.5473 Evaluate side-chains 305 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 559 PHE Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 916 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 324 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 241 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN C 271 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN K 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.114695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.067493 restraints weight = 56333.355| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.64 r_work: 0.2840 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27890 Z= 0.132 Angle : 0.558 12.695 38006 Z= 0.285 Chirality : 0.043 0.169 4422 Planarity : 0.004 0.033 4806 Dihedral : 5.017 58.195 4493 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.69 % Allowed : 13.19 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.14), residues: 3343 helix: 3.04 (0.20), residues: 634 sheet: 1.04 (0.16), residues: 929 loop : -0.36 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.031 0.001 TYR K 756 PHE 0.021 0.001 PHE K 377 TRP 0.035 0.001 TRP F 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00306 (27809) covalent geometry : angle 0.54885 (37805) SS BOND : bond 0.00549 ( 42) SS BOND : angle 1.27517 ( 84) hydrogen bonds : bond 0.04666 ( 1138) hydrogen bonds : angle 5.06782 ( 3162) link_BETA1-4 : bond 0.00304 ( 9) link_BETA1-4 : angle 1.49436 ( 27) link_NAG-ASN : bond 0.00304 ( 30) link_NAG-ASN : angle 1.68962 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 276 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9090 (p0) cc_final: 0.8862 (p0) REVERT: A 73 ASP cc_start: 0.8193 (t0) cc_final: 0.7567 (t0) REVERT: B 17 ASP cc_start: 0.8799 (m-30) cc_final: 0.8574 (p0) REVERT: B 81 GLU cc_start: 0.8779 (pm20) cc_final: 0.8570 (pm20) REVERT: B 82 ASP cc_start: 0.8282 (m-30) cc_final: 0.8022 (m-30) REVERT: C 170 TYR cc_start: 0.7922 (t80) cc_final: 0.7486 (t80) REVERT: C 314 GLN cc_start: 0.8976 (tt0) cc_final: 0.8615 (tm-30) REVERT: C 377 PHE cc_start: 0.8585 (t80) cc_final: 0.8371 (t80) REVERT: C 512 VAL cc_start: 0.8458 (t) cc_final: 0.8186 (m) REVERT: C 533 LEU cc_start: 0.8960 (tp) cc_final: 0.8660 (mt) REVERT: C 559 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.8099 (t80) REVERT: C 581 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8707 (p) REVERT: C 645 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8707 (p) REVERT: C 900 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8837 (mtm) REVERT: C 979 ASP cc_start: 0.8445 (t70) cc_final: 0.8136 (t0) REVERT: C 1029 MET cc_start: 0.9572 (tpp) cc_final: 0.9166 (tpp) REVERT: D 16 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.7802 (mpp80) REVERT: D 73 ASP cc_start: 0.8187 (t0) cc_final: 0.7335 (t0) REVERT: D 76 LYS cc_start: 0.9302 (mttp) cc_final: 0.8925 (ttmm) REVERT: D 82 GLN cc_start: 0.8539 (tp40) cc_final: 0.7796 (tp40) REVERT: E 17 ASP cc_start: 0.8673 (m-30) cc_final: 0.8380 (p0) REVERT: E 78 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7969 (tm) REVERT: F 170 TYR cc_start: 0.7499 (t80) cc_final: 0.7105 (t80) REVERT: F 200 TYR cc_start: 0.8408 (m-80) cc_final: 0.8084 (m-10) REVERT: F 201 PHE cc_start: 0.8296 (t80) cc_final: 0.8051 (t80) REVERT: F 229 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8985 (mt) REVERT: F 265 TYR cc_start: 0.6198 (p90) cc_final: 0.5543 (p90) REVERT: F 314 GLN cc_start: 0.9037 (tt0) cc_final: 0.8739 (tm-30) REVERT: F 512 VAL cc_start: 0.8506 (t) cc_final: 0.8231 (m) REVERT: F 533 LEU cc_start: 0.9045 (tp) cc_final: 0.8749 (mt) REVERT: F 559 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8047 (t80) REVERT: F 581 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8751 (p) REVERT: F 979 ASP cc_start: 0.8675 (t0) cc_final: 0.8434 (t0) REVERT: F 988 GLU cc_start: 0.8627 (mp0) cc_final: 0.8381 (mp0) REVERT: I 30 ASP cc_start: 0.9049 (p0) cc_final: 0.8833 (p0) REVERT: I 73 ASP cc_start: 0.8172 (t0) cc_final: 0.7437 (t0) REVERT: J 24 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7779 (mtp-110) REVERT: K 170 TYR cc_start: 0.7768 (t80) cc_final: 0.7416 (t80) REVERT: K 189 LEU cc_start: 0.9268 (pp) cc_final: 0.8834 (tp) REVERT: K 200 TYR cc_start: 0.8566 (m-80) cc_final: 0.8201 (m-10) REVERT: K 314 GLN cc_start: 0.8929 (tt0) cc_final: 0.8529 (tm-30) REVERT: K 377 PHE cc_start: 0.8596 (t80) cc_final: 0.8208 (t80) REVERT: K 512 VAL cc_start: 0.8471 (t) cc_final: 0.8203 (m) REVERT: K 533 LEU cc_start: 0.9031 (tp) cc_final: 0.8674 (mt) REVERT: K 559 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8071 (t80) REVERT: K 581 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8704 (p) REVERT: K 957 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8794 (tt0) outliers start: 80 outliers final: 45 residues processed: 340 average time/residue: 0.5173 time to fit residues: 208.2598 Evaluate side-chains 312 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 378 LYS Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 559 PHE Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 957 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 27 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS F 218 GLN K 207 HIS K 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.114235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.066787 restraints weight = 56002.605| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.64 r_work: 0.2834 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27890 Z= 0.150 Angle : 0.568 16.167 38006 Z= 0.289 Chirality : 0.044 0.181 4422 Planarity : 0.004 0.045 4806 Dihedral : 5.004 58.669 4493 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.49 % Allowed : 13.72 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.14), residues: 3343 helix: 3.01 (0.20), residues: 634 sheet: 1.03 (0.16), residues: 964 loop : -0.40 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 18 TYR 0.035 0.001 TYR K 756 PHE 0.018 0.001 PHE F 400 TRP 0.041 0.002 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00355 (27809) covalent geometry : angle 0.55914 (37805) SS BOND : bond 0.00577 ( 42) SS BOND : angle 1.18916 ( 84) hydrogen bonds : bond 0.04777 ( 1138) hydrogen bonds : angle 5.00203 ( 3162) link_BETA1-4 : bond 0.00300 ( 9) link_BETA1-4 : angle 1.49370 ( 27) link_NAG-ASN : bond 0.00263 ( 30) link_NAG-ASN : angle 1.64325 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 273 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9107 (p0) cc_final: 0.8884 (p0) REVERT: A 73 ASP cc_start: 0.8219 (t0) cc_final: 0.7555 (t0) REVERT: B 17 ASP cc_start: 0.8741 (m-30) cc_final: 0.8516 (p0) REVERT: C 170 TYR cc_start: 0.8111 (t80) cc_final: 0.7767 (t80) REVERT: C 314 GLN cc_start: 0.9005 (tt0) cc_final: 0.8642 (tm-30) REVERT: C 512 VAL cc_start: 0.8446 (t) cc_final: 0.8150 (m) REVERT: C 533 LEU cc_start: 0.8946 (tp) cc_final: 0.8503 (mt) REVERT: C 559 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8123 (t80) REVERT: C 581 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8698 (p) REVERT: C 645 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8690 (p) REVERT: C 979 ASP cc_start: 0.8446 (t70) cc_final: 0.8126 (t0) REVERT: C 1029 MET cc_start: 0.9568 (tpp) cc_final: 0.9159 (tpp) REVERT: D 73 ASP cc_start: 0.8224 (t0) cc_final: 0.7369 (t0) REVERT: D 76 LYS cc_start: 0.9305 (mttp) cc_final: 0.8941 (ttmm) REVERT: D 82 GLN cc_start: 0.8530 (tp40) cc_final: 0.7784 (tp40) REVERT: E 17 ASP cc_start: 0.8690 (m-30) cc_final: 0.8410 (p0) REVERT: E 78 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8124 (tm) REVERT: F 170 TYR cc_start: 0.7706 (t80) cc_final: 0.7314 (t80) REVERT: F 200 TYR cc_start: 0.8387 (m-80) cc_final: 0.8050 (m-80) REVERT: F 201 PHE cc_start: 0.8329 (t80) cc_final: 0.8096 (t80) REVERT: F 229 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8980 (mt) REVERT: F 314 GLN cc_start: 0.9046 (tt0) cc_final: 0.8749 (tm-30) REVERT: F 512 VAL cc_start: 0.8508 (t) cc_final: 0.8215 (m) REVERT: F 533 LEU cc_start: 0.9039 (tp) cc_final: 0.8767 (mt) REVERT: F 559 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8054 (t80) REVERT: F 581 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8767 (p) REVERT: F 979 ASP cc_start: 0.8687 (t0) cc_final: 0.8435 (t0) REVERT: F 988 GLU cc_start: 0.8640 (mp0) cc_final: 0.8352 (mp0) REVERT: I 16 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7794 (mpp80) REVERT: I 30 ASP cc_start: 0.9119 (p0) cc_final: 0.8906 (p0) REVERT: I 73 ASP cc_start: 0.8251 (t0) cc_final: 0.7491 (t0) REVERT: I 89 GLU cc_start: 0.8989 (mp0) cc_final: 0.8779 (pm20) REVERT: J 24 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7780 (mtp-110) REVERT: K 170 TYR cc_start: 0.7912 (t80) cc_final: 0.7586 (t80) REVERT: K 189 LEU cc_start: 0.9267 (pp) cc_final: 0.8808 (tp) REVERT: K 200 TYR cc_start: 0.8586 (m-80) cc_final: 0.8178 (m-10) REVERT: K 314 GLN cc_start: 0.8934 (tt0) cc_final: 0.8518 (tm-30) REVERT: K 377 PHE cc_start: 0.8643 (t80) cc_final: 0.8298 (t80) REVERT: K 512 VAL cc_start: 0.8488 (t) cc_final: 0.8216 (m) REVERT: K 532 ASN cc_start: 0.9217 (t0) cc_final: 0.9005 (t0) REVERT: K 533 LEU cc_start: 0.9039 (tp) cc_final: 0.8432 (mt) REVERT: K 559 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8135 (t80) REVERT: K 581 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8709 (p) REVERT: K 645 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8430 (p) REVERT: K 855 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: K 957 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8798 (tt0) REVERT: K 988 GLU cc_start: 0.8665 (mp0) cc_final: 0.8219 (mp0) outliers start: 74 outliers final: 43 residues processed: 328 average time/residue: 0.5019 time to fit residues: 196.1211 Evaluate side-chains 308 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 559 PHE Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 645 THR Chi-restraints excluded: chain K residue 855 PHE Chi-restraints excluded: chain K residue 916 LEU Chi-restraints excluded: chain K residue 957 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 173 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 325 optimal weight: 2.9990 chunk 259 optimal weight: 0.5980 chunk 321 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN C 271 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.112996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065497 restraints weight = 55773.624| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.61 r_work: 0.2808 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27890 Z= 0.200 Angle : 0.592 10.094 38006 Z= 0.303 Chirality : 0.045 0.185 4422 Planarity : 0.004 0.046 4806 Dihedral : 5.150 59.710 4493 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.05 % Allowed : 14.43 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.14), residues: 3343 helix: 2.82 (0.20), residues: 638 sheet: 0.96 (0.16), residues: 970 loop : -0.45 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 18 TYR 0.041 0.002 TYR F 265 PHE 0.018 0.002 PHE F 898 TRP 0.044 0.002 TRP F 353 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00480 (27809) covalent geometry : angle 0.58378 (37805) SS BOND : bond 0.00524 ( 42) SS BOND : angle 1.24484 ( 84) hydrogen bonds : bond 0.05222 ( 1138) hydrogen bonds : angle 5.06995 ( 3162) link_BETA1-4 : bond 0.00277 ( 9) link_BETA1-4 : angle 1.56500 ( 27) link_NAG-ASN : bond 0.00260 ( 30) link_NAG-ASN : angle 1.68467 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8260 (t0) cc_final: 0.7629 (t0) REVERT: B 17 ASP cc_start: 0.8780 (m-30) cc_final: 0.8510 (p0) REVERT: C 170 TYR cc_start: 0.8227 (t80) cc_final: 0.7935 (t80) REVERT: C 229 LEU cc_start: 0.8944 (mm) cc_final: 0.8657 (mt) REVERT: C 314 GLN cc_start: 0.9044 (tt0) cc_final: 0.8659 (tm-30) REVERT: C 421 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: C 512 VAL cc_start: 0.8442 (t) cc_final: 0.8128 (m) REVERT: C 533 LEU cc_start: 0.8885 (tp) cc_final: 0.8517 (mt) REVERT: C 559 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8078 (t80) REVERT: C 581 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8711 (p) REVERT: C 979 ASP cc_start: 0.8465 (t70) cc_final: 0.8150 (t0) REVERT: C 1029 MET cc_start: 0.9571 (tpp) cc_final: 0.9208 (tpp) REVERT: D 16 ARG cc_start: 0.8485 (tpp-160) cc_final: 0.7902 (mpp80) REVERT: D 73 ASP cc_start: 0.8279 (t0) cc_final: 0.7413 (t0) REVERT: E 17 ASP cc_start: 0.8731 (m-30) cc_final: 0.8258 (OUTLIER) REVERT: E 78 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8088 (tm) REVERT: F 170 TYR cc_start: 0.7814 (t80) cc_final: 0.7413 (t80) REVERT: F 200 TYR cc_start: 0.8381 (m-80) cc_final: 0.8066 (m-80) REVERT: F 314 GLN cc_start: 0.9082 (tt0) cc_final: 0.8740 (tm-30) REVERT: F 377 PHE cc_start: 0.8724 (t80) cc_final: 0.8467 (t80) REVERT: F 512 VAL cc_start: 0.8538 (t) cc_final: 0.8265 (m) REVERT: F 533 LEU cc_start: 0.9063 (tp) cc_final: 0.8729 (mt) REVERT: F 559 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8104 (t80) REVERT: F 581 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8770 (p) REVERT: F 979 ASP cc_start: 0.8704 (t0) cc_final: 0.8470 (t0) REVERT: F 988 GLU cc_start: 0.8622 (mp0) cc_final: 0.8331 (mp0) REVERT: I 30 ASP cc_start: 0.9168 (p0) cc_final: 0.8946 (p0) REVERT: I 73 ASP cc_start: 0.8299 (t0) cc_final: 0.7519 (t0) REVERT: I 89 GLU cc_start: 0.9105 (mp0) cc_final: 0.8788 (pm20) REVERT: J 24 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7754 (mtp-110) REVERT: K 170 TYR cc_start: 0.7918 (t80) cc_final: 0.7606 (t80) REVERT: K 189 LEU cc_start: 0.9270 (pp) cc_final: 0.8770 (tp) REVERT: K 200 TYR cc_start: 0.8607 (m-80) cc_final: 0.8119 (m-10) REVERT: K 314 GLN cc_start: 0.8955 (tt0) cc_final: 0.8532 (tm-30) REVERT: K 377 PHE cc_start: 0.8804 (t80) cc_final: 0.8485 (t80) REVERT: K 378 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8583 (pttp) REVERT: K 512 VAL cc_start: 0.8484 (t) cc_final: 0.8212 (m) REVERT: K 532 ASN cc_start: 0.9190 (t0) cc_final: 0.8966 (t0) REVERT: K 533 LEU cc_start: 0.9020 (tp) cc_final: 0.8449 (mt) REVERT: K 559 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8151 (t80) REVERT: K 581 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8647 (p) REVERT: K 645 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8451 (p) REVERT: K 957 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: K 988 GLU cc_start: 0.8634 (mp0) cc_final: 0.8194 (mp0) outliers start: 61 outliers final: 38 residues processed: 317 average time/residue: 0.5488 time to fit residues: 207.7821 Evaluate side-chains 301 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 378 LYS Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 559 PHE Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 645 THR Chi-restraints excluded: chain K residue 916 LEU Chi-restraints excluded: chain K residue 957 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 236 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 214 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 203 optimal weight: 0.5980 chunk 251 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN I 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.112994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064471 restraints weight = 54480.997| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.65 r_work: 0.2730 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27890 Z= 0.117 Angle : 0.560 10.613 38006 Z= 0.284 Chirality : 0.043 0.197 4422 Planarity : 0.003 0.041 4806 Dihedral : 4.989 59.269 4493 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.88 % Allowed : 15.04 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.14), residues: 3343 helix: 3.09 (0.20), residues: 635 sheet: 0.95 (0.15), residues: 984 loop : -0.42 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 18 TYR 0.039 0.001 TYR K 756 PHE 0.023 0.001 PHE C 855 TRP 0.042 0.002 TRP K 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00266 (27809) covalent geometry : angle 0.55321 (37805) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.03471 ( 84) hydrogen bonds : bond 0.04460 ( 1138) hydrogen bonds : angle 4.85499 ( 3162) link_BETA1-4 : bond 0.00367 ( 9) link_BETA1-4 : angle 1.40596 ( 27) link_NAG-ASN : bond 0.00261 ( 30) link_NAG-ASN : angle 1.50231 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8361 (tpp-160) cc_final: 0.7720 (mpp80) REVERT: A 73 ASP cc_start: 0.8224 (t0) cc_final: 0.7444 (t0) REVERT: C 170 TYR cc_start: 0.8267 (t80) cc_final: 0.7867 (t80) REVERT: C 201 PHE cc_start: 0.8424 (t80) cc_final: 0.8218 (t80) REVERT: C 229 LEU cc_start: 0.8980 (mm) cc_final: 0.8660 (mt) REVERT: C 314 GLN cc_start: 0.9036 (tt0) cc_final: 0.8677 (tm-30) REVERT: C 512 VAL cc_start: 0.8367 (t) cc_final: 0.8052 (m) REVERT: C 533 LEU cc_start: 0.8824 (tp) cc_final: 0.8587 (mt) REVERT: C 559 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8084 (t80) REVERT: C 581 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 645 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 979 ASP cc_start: 0.8492 (t70) cc_final: 0.8180 (t0) REVERT: C 1029 MET cc_start: 0.9561 (tpp) cc_final: 0.9150 (tpp) REVERT: D 16 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.7894 (mpp80) REVERT: D 73 ASP cc_start: 0.8217 (t0) cc_final: 0.7264 (t0) REVERT: E 17 ASP cc_start: 0.8663 (m-30) cc_final: 0.8339 (OUTLIER) REVERT: E 78 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7972 (tm) REVERT: F 170 TYR cc_start: 0.7590 (t80) cc_final: 0.7301 (t80) REVERT: F 200 TYR cc_start: 0.8373 (m-80) cc_final: 0.8068 (m-80) REVERT: F 314 GLN cc_start: 0.9050 (tt0) cc_final: 0.8766 (tm-30) REVERT: F 353 TRP cc_start: 0.8411 (p-90) cc_final: 0.8140 (p-90) REVERT: F 430 THR cc_start: 0.8556 (p) cc_final: 0.8352 (t) REVERT: F 512 VAL cc_start: 0.8430 (t) cc_final: 0.8154 (m) REVERT: F 533 LEU cc_start: 0.9025 (tp) cc_final: 0.8718 (mt) REVERT: F 559 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8057 (t80) REVERT: F 581 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8754 (p) REVERT: F 979 ASP cc_start: 0.8738 (t0) cc_final: 0.8476 (OUTLIER) REVERT: F 988 GLU cc_start: 0.8680 (mp0) cc_final: 0.8371 (mp0) REVERT: I 16 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.7811 (mpp80) REVERT: I 73 ASP cc_start: 0.8201 (t0) cc_final: 0.7398 (t0) REVERT: I 76 LYS cc_start: 0.9287 (mttp) cc_final: 0.8982 (mtmt) REVERT: I 87 ARG cc_start: 0.8275 (mpp80) cc_final: 0.7850 (mpp80) REVERT: I 89 GLU cc_start: 0.9099 (mp0) cc_final: 0.8785 (pm20) REVERT: J 24 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7778 (mtp-110) REVERT: J 103 LYS cc_start: 0.8622 (tppp) cc_final: 0.8369 (tptm) REVERT: K 170 TYR cc_start: 0.7880 (t80) cc_final: 0.7451 (t80) REVERT: K 189 LEU cc_start: 0.9259 (pp) cc_final: 0.8764 (tp) REVERT: K 200 TYR cc_start: 0.8559 (m-80) cc_final: 0.8091 (m-10) REVERT: K 314 GLN cc_start: 0.8958 (tt0) cc_final: 0.8576 (tm-30) REVERT: K 377 PHE cc_start: 0.8814 (t80) cc_final: 0.8601 (t80) REVERT: K 512 VAL cc_start: 0.8373 (t) cc_final: 0.8105 (m) REVERT: K 532 ASN cc_start: 0.9194 (t0) cc_final: 0.8964 (t0) REVERT: K 533 LEU cc_start: 0.9014 (tp) cc_final: 0.8442 (mt) REVERT: K 581 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8701 (p) REVERT: K 645 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8451 (p) REVERT: K 957 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8811 (tt0) REVERT: K 988 GLU cc_start: 0.8656 (mp0) cc_final: 0.8226 (mp0) outliers start: 56 outliers final: 35 residues processed: 312 average time/residue: 0.5532 time to fit residues: 203.5850 Evaluate side-chains 294 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 378 LYS Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 645 THR Chi-restraints excluded: chain K residue 957 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 325 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 299 optimal weight: 0.0770 chunk 122 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 271 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN K 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.113073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.064650 restraints weight = 54670.414| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.62 r_work: 0.2740 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27890 Z= 0.119 Angle : 0.564 10.498 38006 Z= 0.287 Chirality : 0.043 0.195 4422 Planarity : 0.004 0.040 4806 Dihedral : 4.949 59.433 4493 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.58 % Allowed : 15.37 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.14), residues: 3343 helix: 3.09 (0.20), residues: 641 sheet: 0.95 (0.16), residues: 975 loop : -0.39 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 18 TYR 0.039 0.001 TYR K 756 PHE 0.022 0.001 PHE C 92 TRP 0.039 0.002 TRP F 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00275 (27809) covalent geometry : angle 0.55704 (37805) SS BOND : bond 0.00452 ( 42) SS BOND : angle 1.00930 ( 84) hydrogen bonds : bond 0.04390 ( 1138) hydrogen bonds : angle 4.82288 ( 3162) link_BETA1-4 : bond 0.00362 ( 9) link_BETA1-4 : angle 1.37953 ( 27) link_NAG-ASN : bond 0.00258 ( 30) link_NAG-ASN : angle 1.50781 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.7719 (mpp80) REVERT: A 73 ASP cc_start: 0.8188 (t0) cc_final: 0.7395 (t0) REVERT: C 170 TYR cc_start: 0.8211 (t80) cc_final: 0.7816 (t80) REVERT: C 201 PHE cc_start: 0.8453 (t80) cc_final: 0.8235 (t80) REVERT: C 229 LEU cc_start: 0.8943 (mm) cc_final: 0.8592 (mt) REVERT: C 314 GLN cc_start: 0.9028 (tt0) cc_final: 0.8664 (tm-30) REVERT: C 512 VAL cc_start: 0.8380 (t) cc_final: 0.8063 (m) REVERT: C 533 LEU cc_start: 0.8821 (tp) cc_final: 0.8551 (mt) REVERT: C 559 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8063 (t80) REVERT: C 581 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8678 (p) REVERT: C 645 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8634 (p) REVERT: C 979 ASP cc_start: 0.8470 (t70) cc_final: 0.8156 (t0) REVERT: C 1029 MET cc_start: 0.9546 (tpp) cc_final: 0.9112 (tpp) REVERT: D 16 ARG cc_start: 0.8485 (tpp-160) cc_final: 0.7890 (mpp80) REVERT: D 73 ASP cc_start: 0.8176 (t0) cc_final: 0.7215 (t0) REVERT: E 17 ASP cc_start: 0.8657 (m-30) cc_final: 0.8345 (p0) REVERT: E 78 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7886 (tm) REVERT: F 170 TYR cc_start: 0.7769 (t80) cc_final: 0.7478 (t80) REVERT: F 200 TYR cc_start: 0.8369 (m-80) cc_final: 0.8052 (m-80) REVERT: F 314 GLN cc_start: 0.9043 (tt0) cc_final: 0.8754 (tm-30) REVERT: F 353 TRP cc_start: 0.8406 (p-90) cc_final: 0.8118 (p-90) REVERT: F 430 THR cc_start: 0.8545 (p) cc_final: 0.8337 (t) REVERT: F 512 VAL cc_start: 0.8390 (t) cc_final: 0.8070 (m) REVERT: F 533 LEU cc_start: 0.9018 (tp) cc_final: 0.8717 (mt) REVERT: F 559 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.8036 (t80) REVERT: F 581 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8752 (p) REVERT: F 979 ASP cc_start: 0.8743 (t0) cc_final: 0.8488 (OUTLIER) REVERT: F 988 GLU cc_start: 0.8673 (mp0) cc_final: 0.8355 (mp0) REVERT: I 16 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.7850 (mpp80) REVERT: I 73 ASP cc_start: 0.8169 (t0) cc_final: 0.7337 (t0) REVERT: I 76 LYS cc_start: 0.9276 (mttp) cc_final: 0.8968 (mtmt) REVERT: I 87 ARG cc_start: 0.8262 (mpp80) cc_final: 0.7847 (mpp80) REVERT: I 89 GLU cc_start: 0.9096 (mp0) cc_final: 0.8782 (pm20) REVERT: J 24 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7774 (mtp-110) REVERT: J 103 LYS cc_start: 0.8597 (tppp) cc_final: 0.8339 (tptm) REVERT: K 170 TYR cc_start: 0.7863 (t80) cc_final: 0.7468 (t80) REVERT: K 189 LEU cc_start: 0.9211 (pp) cc_final: 0.8741 (tp) REVERT: K 200 TYR cc_start: 0.8512 (m-80) cc_final: 0.8033 (m-10) REVERT: K 314 GLN cc_start: 0.8941 (tt0) cc_final: 0.8582 (tm-30) REVERT: K 377 PHE cc_start: 0.8833 (t80) cc_final: 0.8622 (t80) REVERT: K 512 VAL cc_start: 0.8429 (t) cc_final: 0.8163 (m) REVERT: K 532 ASN cc_start: 0.9188 (t0) cc_final: 0.8956 (t0) REVERT: K 533 LEU cc_start: 0.9020 (tp) cc_final: 0.8449 (mt) REVERT: K 581 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8704 (p) REVERT: K 645 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8428 (p) REVERT: K 957 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8776 (tt0) REVERT: K 988 GLU cc_start: 0.8629 (mp0) cc_final: 0.8181 (mp0) outliers start: 47 outliers final: 33 residues processed: 303 average time/residue: 0.6057 time to fit residues: 216.5196 Evaluate side-chains 294 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 378 LYS Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 645 THR Chi-restraints excluded: chain K residue 957 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 218 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 277 optimal weight: 0.0040 chunk 32 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 27 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 307 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.112562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063954 restraints weight = 54396.029| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.64 r_work: 0.2728 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27890 Z= 0.143 Angle : 0.579 10.897 38006 Z= 0.295 Chirality : 0.044 0.200 4422 Planarity : 0.004 0.041 4806 Dihedral : 4.948 59.494 4493 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.58 % Allowed : 15.67 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.14), residues: 3343 helix: 3.10 (0.20), residues: 637 sheet: 0.96 (0.16), residues: 975 loop : -0.43 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 18 TYR 0.039 0.001 TYR K 756 PHE 0.028 0.001 PHE F 194 TRP 0.053 0.002 TRP C 353 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00338 (27809) covalent geometry : angle 0.57272 (37805) SS BOND : bond 0.00450 ( 42) SS BOND : angle 1.02943 ( 84) hydrogen bonds : bond 0.04585 ( 1138) hydrogen bonds : angle 4.83956 ( 3162) link_BETA1-4 : bond 0.00315 ( 9) link_BETA1-4 : angle 1.41559 ( 27) link_NAG-ASN : bond 0.00244 ( 30) link_NAG-ASN : angle 1.53272 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13746.14 seconds wall clock time: 233 minutes 46.91 seconds (14026.91 seconds total)