Starting phenix.real_space_refine on Mon Jun 23 15:32:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhy_46892/06_2025/9dhy_46892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhy_46892/06_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_46892/06_2025/9dhy_46892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhy_46892/06_2025/9dhy_46892.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhy_46892/06_2025/9dhy_46892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhy_46892/06_2025/9dhy_46892.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.43, per 1000 atoms: 0.64 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: 7.38 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 4.90 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: 13.98 Time building geometry restraints manager: 8.78 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 1145 or resid 1301 thr \ ough 1307)) selection = (chain 'K' and (resid 28 through 107 or resid 116 through 1145 or resid 1301 thr \ ough 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: 5.080 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: 0.050 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 69.600 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.160 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:15.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.830 ------------------------------------------------------------------------------- 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 : 6.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.022 0.003 TRP K 104 HIS 0.018 0.004 HIS F1064 PHE 0.033 0.004 PHE K 543 TYR 0.048 0.003 TYR K 789 ARG 0.006 0.001 ARG F1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00853 ( 30) link_NAG-ASN : angle 4.77775 ( 90) link_BETA1-4 : bond 0.00391 ( 9) link_BETA1-4 : angle 3.11499 ( 27) hydrogen bonds : bond 0.20165 ( 1138) hydrogen bonds : angle 8.46997 ( 3162) SS BOND : bond 0.00538 ( 42) SS BOND : angle 1.19784 ( 84) covalent geometry : bond 0.01362 (27809) covalent geometry : angle 1.03137 (37805) *********************** 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 : 2.965 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: 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: 0.8406 (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: 0.8408 (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: 0.7768 (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: 0.7933 (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 265 TYR cc_start: 0.6763 (p90) cc_final: 0.5903 (p90) REVERT: F 269 TYR cc_start: 0.7922 (m-80) cc_final: 0.7662 (m-80) REVERT: F 360 ASN cc_start: 0.9025 (t0) cc_final: 0.8553 (t0) REVERT: F 392 PHE cc_start: 0.8262 (m-80) cc_final: 0.8010 (m-80) REVERT: F 400 PHE cc_start: 0.8779 (p90) cc_final: 0.8452 (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: 0.7758 (mt-10) 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: 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: 0.8584 (t0) REVERT: K 396 TYR cc_start: 0.7303 (m-80) cc_final: 0.6639 (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 543 PHE cc_start: 0.7475 (m-10) cc_final: 0.7241 (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: 1.2589 time to fit residues: 815.5388 Evaluate side-chains 313 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 290 time to evaluate : 3.055 ------------------------------------------------------------------------------- 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 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 286 optimal weight: 9.9990 chunk 256 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 173 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN C 613 GLN C 762 GLN C 955 ASN F 87 ASN F 218 GLN F 613 GLN F 762 GLN ** F 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 218 GLN K 613 GLN K 762 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.114857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066762 restraints weight = 55398.968| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.67 r_work: 0.2837 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27890 Z= 0.183 Angle : 0.660 12.221 38006 Z= 0.342 Chirality : 0.047 0.222 4422 Planarity : 0.004 0.029 4806 Dihedral : 5.827 59.011 4522 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.39 % Allowed : 11.34 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.14), residues: 3343 helix: 2.80 (0.20), residues: 633 sheet: 1.76 (0.17), residues: 811 loop : -0.20 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 436 HIS 0.006 0.001 HIS C1064 PHE 0.018 0.002 PHE F 58 TYR 0.034 0.002 TYR K 265 ARG 0.005 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 30) link_NAG-ASN : angle 2.35096 ( 90) link_BETA1-4 : bond 0.00396 ( 9) link_BETA1-4 : angle 1.70780 ( 27) hydrogen bonds : bond 0.05834 ( 1138) hydrogen bonds : angle 5.97733 ( 3162) SS BOND : bond 0.00641 ( 42) SS BOND : angle 2.10236 ( 84) covalent geometry : bond 0.00427 (27809) covalent geometry : angle 0.64277 (37805) *********************** 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 416 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 345 time to evaluate : 2.829 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 89 GLU cc_start: 0.8484 (pm20) cc_final: 0.8255 (pm20) REVERT: B 103 LYS cc_start: 0.8657 (tppp) cc_final: 0.8425 (tppp) REVERT: C 64 TRP cc_start: 0.7689 (t-100) cc_final: 0.7464 (t60) REVERT: C 201 PHE cc_start: 0.8309 (t80) cc_final: 0.8098 (t80) REVERT: C 314 GLN cc_start: 0.8740 (tt0) cc_final: 0.8360 (tm-30) REVERT: C 360 ASN cc_start: 0.8686 (t0) cc_final: 0.8469 (t0) REVERT: C 374 PHE cc_start: 0.8566 (m-80) cc_final: 0.8364 (m-80) REVERT: C 378 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8344 (ptmm) REVERT: C 400 PHE cc_start: 0.8823 (p90) cc_final: 0.8615 (p90) REVERT: C 421 TYR cc_start: 0.7172 (m-80) cc_final: 0.6467 (m-10) REVERT: C 512 VAL cc_start: 0.8439 (t) cc_final: 0.8086 (m) REVERT: C 533 LEU cc_start: 0.8953 (tp) cc_final: 0.8627 (mt) REVERT: C 559 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7861 (t80) REVERT: C 565 PHE cc_start: 0.7784 (m-80) cc_final: 0.7576 (m-10) REVERT: C 979 ASP cc_start: 0.8386 (t70) cc_final: 0.8002 (t0) REVERT: C 988 GLU cc_start: 0.8617 (mp0) cc_final: 0.8288 (mp0) REVERT: C 1029 MET cc_start: 0.9528 (tpp) cc_final: 0.9219 (tpp) REVERT: D 82 GLN cc_start: 0.8321 (tp40) cc_final: 0.7922 (tp40) REVERT: D 89 GLU cc_start: 0.8541 (pm20) cc_final: 0.8334 (pm20) REVERT: E 105 GLU cc_start: 0.5115 (tm-30) cc_final: 0.4914 (tm-30) REVERT: F 87 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.6965 (p0) REVERT: F 201 PHE cc_start: 0.8209 (t80) cc_final: 0.7923 (t80) REVERT: F 265 TYR cc_start: 0.6381 (p90) cc_final: 0.5697 (p90) REVERT: F 314 GLN cc_start: 0.8968 (tt0) cc_final: 0.8534 (tm-30) REVERT: F 360 ASN cc_start: 0.8803 (t0) cc_final: 0.8569 (t0) REVERT: F 374 PHE cc_start: 0.8539 (m-80) cc_final: 0.8310 (m-80) REVERT: F 378 LYS cc_start: 0.8938 (ptpp) cc_final: 0.8544 (ptmm) REVERT: F 400 PHE cc_start: 0.8723 (p90) cc_final: 0.8521 (p90) REVERT: F 512 VAL cc_start: 0.8403 (t) cc_final: 0.8120 (m) REVERT: F 516 GLU cc_start: 0.7816 (tt0) cc_final: 0.7458 (mt-10) REVERT: F 988 GLU cc_start: 0.8491 (mp0) cc_final: 0.8153 (mp0) REVERT: I 30 ASP cc_start: 0.8907 (p0) cc_final: 0.8640 (p0) REVERT: I 32 TYR cc_start: 0.9192 (m-80) cc_final: 0.8970 (m-80) REVERT: I 82 GLN cc_start: 0.8341 (tp40) cc_final: 0.8135 (tp40) REVERT: I 89 GLU cc_start: 0.8602 (pm20) cc_final: 0.8261 (pm20) REVERT: K 314 GLN cc_start: 0.8782 (tt0) cc_final: 0.8257 (tm-30) REVERT: K 357 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.8027 (ttp80) REVERT: K 360 ASN cc_start: 0.8974 (t0) cc_final: 0.8497 (t0) REVERT: K 377 PHE cc_start: 0.8399 (t80) cc_final: 0.7960 (t80) REVERT: K 378 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8404 (ptmm) REVERT: K 512 VAL cc_start: 0.8320 (t) cc_final: 0.8017 (m) REVERT: K 516 GLU cc_start: 0.7849 (tt0) cc_final: 0.7409 (mt-10) REVERT: K 979 ASP cc_start: 0.8504 (t0) cc_final: 0.8288 (t0) outliers start: 71 outliers final: 22 residues processed: 399 average time/residue: 1.3595 time to fit residues: 648.4412 Evaluate side-chains 285 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 3.228 ------------------------------------------------------------------------------- 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 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 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 265 TYR Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 517 LEU Chi-restraints excluded: chain K residue 900 MET Chi-restraints excluded: chain K residue 916 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 326 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 328 optimal weight: 0.0670 chunk 45 optimal weight: 4.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.112602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064193 restraints weight = 55845.215| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.65 r_work: 0.2774 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 27890 Z= 0.249 Angle : 0.645 10.960 38006 Z= 0.336 Chirality : 0.047 0.180 4422 Planarity : 0.004 0.045 4806 Dihedral : 5.523 59.553 4493 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.62 % Allowed : 12.24 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3343 helix: 2.64 (0.20), residues: 637 sheet: 1.31 (0.16), residues: 890 loop : -0.37 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 436 HIS 0.010 0.002 HIS C1064 PHE 0.019 0.002 PHE F 898 TYR 0.044 0.002 TYR K 265 ARG 0.009 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 30) link_NAG-ASN : angle 2.18273 ( 90) link_BETA1-4 : bond 0.00249 ( 9) link_BETA1-4 : angle 1.74580 ( 27) hydrogen bonds : bond 0.06023 ( 1138) hydrogen bonds : angle 5.67896 ( 3162) SS BOND : bond 0.00512 ( 42) SS BOND : angle 1.55418 ( 84) covalent geometry : bond 0.00597 (27809) covalent geometry : angle 0.63242 (37805) *********************** 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 369 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 291 time to evaluate : 4.673 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: 0.8144 (t0) cc_final: 0.7454 (t0) REVERT: A 89 GLU cc_start: 0.8472 (pm20) cc_final: 0.8175 (pm20) REVERT: C 170 TYR cc_start: 0.7866 (t80) cc_final: 0.7547 (t80) REVERT: C 200 TYR cc_start: 0.8348 (m-80) cc_final: 0.7692 (m-80) REVERT: C 201 PHE cc_start: 0.8403 (t80) cc_final: 0.8069 (t80) REVERT: C 314 GLN cc_start: 0.8953 (tt0) cc_final: 0.8505 (tm-30) REVERT: C 360 ASN cc_start: 0.8681 (t0) cc_final: 0.8197 (t0) REVERT: C 374 PHE cc_start: 0.8727 (m-80) cc_final: 0.8443 (m-80) REVERT: C 378 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8765 (ptmm) REVERT: C 421 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6572 (m-80) REVERT: C 512 VAL cc_start: 0.8406 (t) cc_final: 0.8119 (m) REVERT: C 533 LEU cc_start: 0.8998 (tp) cc_final: 0.8639 (mt) REVERT: C 565 PHE cc_start: 0.7859 (m-80) cc_final: 0.7632 (m-10) REVERT: C 894 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9207 (mt) REVERT: C 979 ASP cc_start: 0.8416 (t70) cc_final: 0.8018 (t0) REVERT: C 1029 MET cc_start: 0.9497 (tpp) cc_final: 0.9153 (tpp) REVERT: D 73 ASP cc_start: 0.8136 (t0) cc_final: 0.7345 (t0) REVERT: D 82 GLN cc_start: 0.8402 (tp40) cc_final: 0.7977 (tp40) REVERT: D 89 GLU cc_start: 0.8594 (pm20) cc_final: 0.8369 (pm20) REVERT: F 170 TYR cc_start: 0.7777 (t80) cc_final: 0.7521 (t80) REVERT: F 200 TYR cc_start: 0.8274 (m-10) cc_final: 0.8069 (m-10) REVERT: F 201 PHE cc_start: 0.8209 (t80) cc_final: 0.7780 (t80) REVERT: F 265 TYR cc_start: 0.6406 (p90) cc_final: 0.5767 (p90) REVERT: F 314 GLN cc_start: 0.9043 (tt0) cc_final: 0.8590 (tm-30) REVERT: F 360 ASN cc_start: 0.8863 (t0) cc_final: 0.8419 (t0) REVERT: F 374 PHE cc_start: 0.8642 (m-80) cc_final: 0.8370 (m-80) REVERT: F 400 PHE cc_start: 0.8826 (p90) cc_final: 0.8600 (p90) REVERT: F 512 VAL cc_start: 0.8462 (t) cc_final: 0.8215 (m) REVERT: F 988 GLU cc_start: 0.8447 (mp0) cc_final: 0.8099 (mp0) REVERT: I 30 ASP cc_start: 0.9035 (p0) cc_final: 0.8774 (p0) REVERT: I 67 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7876 (mtm180) REVERT: I 73 ASP cc_start: 0.8123 (t0) cc_final: 0.7314 (t0) REVERT: I 89 GLU cc_start: 0.8646 (pm20) cc_final: 0.8282 (pm20) REVERT: J 105 GLU cc_start: 0.4883 (tm-30) cc_final: 0.4390 (tm-30) REVERT: K 314 GLN cc_start: 0.8897 (tt0) cc_final: 0.8396 (tm-30) REVERT: K 360 ASN cc_start: 0.8818 (t0) cc_final: 0.8516 (t0) REVERT: K 396 TYR cc_start: 0.7297 (m-10) cc_final: 0.6399 (m-80) REVERT: K 512 VAL cc_start: 0.8403 (t) cc_final: 0.8191 (m) REVERT: K 532 ASN cc_start: 0.9280 (t0) cc_final: 0.9033 (t0) REVERT: K 979 ASP cc_start: 0.8555 (t0) cc_final: 0.8269 (t0) outliers start: 78 outliers final: 27 residues processed: 350 average time/residue: 1.4092 time to fit residues: 583.7720 Evaluate side-chains 286 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 2.952 ------------------------------------------------------------------------------- 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 368 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 894 LEU 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 236 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain K residue 130 VAL 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 453 TYR Chi-restraints excluded: chain K residue 517 LEU Chi-restraints excluded: chain K residue 525 CYS 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 266 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 329 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 58 optimal weight: 0.2980 chunk 143 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.113377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065197 restraints weight = 55728.395| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.67 r_work: 0.2795 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3014 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= 0.163 Angle : 0.588 11.882 38006 Z= 0.300 Chirality : 0.045 0.162 4422 Planarity : 0.004 0.034 4806 Dihedral : 5.270 59.999 4491 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.49 % Allowed : 13.02 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3343 helix: 2.74 (0.20), residues: 638 sheet: 1.11 (0.16), residues: 952 loop : -0.42 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 436 HIS 0.005 0.001 HIS C1064 PHE 0.023 0.002 PHE F 168 TYR 0.031 0.001 TYR C 756 ARG 0.006 0.000 ARG A 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 30) link_NAG-ASN : angle 1.90745 ( 90) link_BETA1-4 : bond 0.00314 ( 9) link_BETA1-4 : angle 1.58524 ( 27) hydrogen bonds : bond 0.05188 ( 1138) hydrogen bonds : angle 5.37105 ( 3162) SS BOND : bond 0.00617 ( 42) SS BOND : angle 1.34897 ( 84) covalent geometry : bond 0.00382 (27809) covalent geometry : angle 0.57665 (37805) *********************** 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 357 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 2.865 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: 0.9081 (p0) cc_final: 0.8859 (p0) REVERT: A 73 ASP cc_start: 0.8073 (t0) cc_final: 0.7454 (t0) REVERT: C 170 TYR cc_start: 0.7989 (t80) cc_final: 0.7612 (t80) REVERT: C 189 LEU cc_start: 0.9025 (pp) cc_final: 0.8712 (tp) REVERT: C 201 PHE cc_start: 0.8317 (t80) cc_final: 0.8093 (t80) REVERT: C 314 GLN cc_start: 0.8955 (tt0) cc_final: 0.8537 (tm-30) REVERT: C 378 LYS cc_start: 0.9108 (ptpp) cc_final: 0.8875 (ptpp) REVERT: C 421 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: C 512 VAL cc_start: 0.8411 (t) cc_final: 0.8122 (m) REVERT: C 533 LEU cc_start: 0.8993 (tp) cc_final: 0.8647 (mt) REVERT: C 565 PHE cc_start: 0.7800 (m-80) cc_final: 0.7572 (m-10) REVERT: C 979 ASP cc_start: 0.8408 (t70) cc_final: 0.8045 (t0) REVERT: C 1029 MET cc_start: 0.9493 (tpp) cc_final: 0.9179 (tpp) REVERT: D 73 ASP cc_start: 0.8041 (t0) cc_final: 0.7127 (t0) REVERT: D 82 GLN cc_start: 0.8401 (tp40) cc_final: 0.7813 (tp40) REVERT: D 89 GLU cc_start: 0.8632 (pm20) cc_final: 0.8388 (pm20) REVERT: E 105 GLU cc_start: 0.5163 (tm-30) cc_final: 0.4862 (tm-30) REVERT: F 189 LEU cc_start: 0.9102 (pp) cc_final: 0.8710 (tp) REVERT: F 200 TYR cc_start: 0.8231 (m-10) cc_final: 0.8009 (m-10) REVERT: F 201 PHE cc_start: 0.8232 (t80) cc_final: 0.7932 (t80) REVERT: F 265 TYR cc_start: 0.6516 (p90) cc_final: 0.5890 (p90) REVERT: F 314 GLN cc_start: 0.8980 (tt0) cc_final: 0.8570 (tm-30) REVERT: F 360 ASN cc_start: 0.8798 (t0) cc_final: 0.8572 (t0) REVERT: F 374 PHE cc_start: 0.8686 (m-80) cc_final: 0.8416 (m-80) REVERT: F 400 PHE cc_start: 0.8936 (p90) cc_final: 0.8702 (p90) REVERT: F 421 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: F 512 VAL cc_start: 0.8447 (t) cc_final: 0.8179 (m) REVERT: F 559 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7829 (t80) REVERT: F 564 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: F 988 GLU cc_start: 0.8511 (mp0) cc_final: 0.8264 (mp0) REVERT: I 30 ASP cc_start: 0.9060 (p0) cc_final: 0.8784 (p0) REVERT: I 73 ASP cc_start: 0.8046 (t0) cc_final: 0.7244 (t0) REVERT: I 87 ARG cc_start: 0.8028 (mpp80) cc_final: 0.7804 (mpp80) REVERT: J 105 GLU cc_start: 0.4730 (tm-30) cc_final: 0.4336 (tm-30) REVERT: K 170 TYR cc_start: 0.7954 (t80) cc_final: 0.7677 (t80) REVERT: K 189 LEU cc_start: 0.9131 (pp) cc_final: 0.8754 (tp) REVERT: K 200 TYR cc_start: 0.8347 (m-80) cc_final: 0.8142 (m-80) REVERT: K 314 GLN cc_start: 0.8899 (tt0) cc_final: 0.8440 (tm-30) REVERT: K 360 ASN cc_start: 0.8852 (t0) cc_final: 0.8651 (t0) REVERT: K 512 VAL cc_start: 0.8387 (t) cc_final: 0.8157 (m) REVERT: K 532 ASN cc_start: 0.9275 (t0) cc_final: 0.9027 (t0) REVERT: K 559 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7828 (t80) REVERT: K 979 ASP cc_start: 0.8570 (t0) cc_final: 0.8257 (t0) outliers start: 74 outliers final: 34 residues processed: 344 average time/residue: 1.1761 time to fit residues: 481.7863 Evaluate side-chains 299 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 130 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 421 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 525 CYS 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 213 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 368 LEU Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 564 GLN 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 94 SER 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 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 Chi-restraints excluded: chain K residue 916 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 67 optimal weight: 5.9990 chunk 201 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 243 optimal weight: 0.0770 chunk 115 optimal weight: 0.6980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 218 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN I 39 GLN J 3 GLN K 207 HIS K 218 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.114525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067210 restraints weight = 56124.026| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.65 r_work: 0.2834 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27890 Z= 0.123 Angle : 0.565 11.474 38006 Z= 0.287 Chirality : 0.044 0.167 4422 Planarity : 0.004 0.038 4806 Dihedral : 5.085 58.332 4491 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.62 % Allowed : 12.92 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3343 helix: 2.96 (0.20), residues: 634 sheet: 1.03 (0.16), residues: 969 loop : -0.40 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP K 436 HIS 0.003 0.001 HIS C1064 PHE 0.025 0.001 PHE K 168 TYR 0.032 0.001 TYR C 756 ARG 0.007 0.000 ARG A 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 30) link_NAG-ASN : angle 1.87328 ( 90) link_BETA1-4 : bond 0.00363 ( 9) link_BETA1-4 : angle 1.48216 ( 27) hydrogen bonds : bond 0.04639 ( 1138) hydrogen bonds : angle 5.15074 ( 3162) SS BOND : bond 0.00497 ( 42) SS BOND : angle 1.22186 ( 84) covalent geometry : bond 0.00280 (27809) covalent geometry : angle 0.55469 (37805) *********************** 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 356 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 278 time to evaluate : 2.749 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: 0.8192 (t0) cc_final: 0.7550 (t0) REVERT: A 87 ARG cc_start: 0.7873 (mpp80) cc_final: 0.7646 (mpp80) REVERT: A 102 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8793 (mt) REVERT: B 70 ASP cc_start: 0.7237 (m-30) cc_final: 0.7023 (m-30) REVERT: C 170 TYR cc_start: 0.7966 (t80) cc_final: 0.7523 (t80) REVERT: C 189 LEU cc_start: 0.8969 (pp) cc_final: 0.8615 (tp) REVERT: C 314 GLN cc_start: 0.8983 (tt0) cc_final: 0.8635 (tm-30) REVERT: C 421 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6550 (m-80) REVERT: C 512 VAL cc_start: 0.8456 (t) cc_final: 0.8188 (m) REVERT: C 533 LEU cc_start: 0.8968 (tp) cc_final: 0.8648 (mt) REVERT: C 559 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7981 (t80) REVERT: C 565 PHE cc_start: 0.7748 (m-80) cc_final: 0.7531 (m-10) REVERT: C 581 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8713 (p) REVERT: C 979 ASP cc_start: 0.8446 (t70) cc_final: 0.8140 (t0) REVERT: C 1029 MET cc_start: 0.9574 (tpp) cc_final: 0.9170 (tpp) REVERT: D 16 ARG cc_start: 0.8363 (tpp-160) cc_final: 0.7807 (mpp80) REVERT: D 73 ASP cc_start: 0.8191 (t0) cc_final: 0.7292 (t0) REVERT: D 82 GLN cc_start: 0.8544 (tp40) cc_final: 0.7772 (tp40) REVERT: D 89 GLU cc_start: 0.8650 (pm20) cc_final: 0.8404 (pm20) REVERT: F 189 LEU cc_start: 0.9095 (pp) cc_final: 0.8640 (tp) REVERT: F 200 TYR cc_start: 0.8227 (m-10) cc_final: 0.7959 (m-10) REVERT: F 201 PHE cc_start: 0.8357 (t80) cc_final: 0.7983 (t80) REVERT: F 265 TYR cc_start: 0.6484 (p90) cc_final: 0.5868 (p90) REVERT: F 314 GLN cc_start: 0.8989 (tt0) cc_final: 0.8709 (tm-30) REVERT: F 360 ASN cc_start: 0.8860 (t0) cc_final: 0.8621 (t0) REVERT: F 374 PHE cc_start: 0.8717 (m-80) cc_final: 0.8475 (m-80) REVERT: F 421 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6650 (m-80) REVERT: F 512 VAL cc_start: 0.8501 (t) cc_final: 0.8234 (m) REVERT: F 559 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8092 (t80) REVERT: F 581 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8789 (p) REVERT: F 900 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8916 (mtm) REVERT: F 988 GLU cc_start: 0.8629 (mp0) cc_final: 0.8334 (mp0) REVERT: I 30 ASP cc_start: 0.9127 (p0) cc_final: 0.8925 (p0) REVERT: I 73 ASP cc_start: 0.8187 (t0) cc_final: 0.7416 (t0) REVERT: I 87 ARG cc_start: 0.8260 (mpp80) cc_final: 0.8013 (mpp80) REVERT: J 24 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7738 (mtp-110) REVERT: J 105 GLU cc_start: 0.4790 (tm-30) cc_final: 0.4454 (tm-30) REVERT: K 170 TYR cc_start: 0.8073 (t80) cc_final: 0.7743 (t80) REVERT: K 189 LEU cc_start: 0.9135 (pp) cc_final: 0.8745 (tp) REVERT: K 314 GLN cc_start: 0.8952 (tt0) cc_final: 0.8552 (tm-30) REVERT: K 512 VAL cc_start: 0.8455 (t) cc_final: 0.8203 (m) REVERT: K 532 ASN cc_start: 0.9284 (t0) cc_final: 0.9039 (t0) REVERT: K 559 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.8025 (t80) REVERT: K 894 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9250 (mt) REVERT: K 979 ASP cc_start: 0.8606 (t0) cc_final: 0.8270 (t0) REVERT: K 988 GLU cc_start: 0.8659 (mp0) cc_final: 0.8233 (mp0) outliers start: 78 outliers final: 38 residues processed: 339 average time/residue: 1.1935 time to fit residues: 480.8597 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 : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 102 LEU 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 127 VAL Chi-restraints excluded: chain C residue 130 VAL 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 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 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 350 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 979 ASP 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 K residue 54 LEU Chi-restraints excluded: chain K residue 94 SER 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 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 894 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 267 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 274 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 207 HIS F 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.113539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065978 restraints weight = 56123.222| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.64 r_work: 0.2811 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27890 Z= 0.167 Angle : 0.580 10.729 38006 Z= 0.295 Chirality : 0.044 0.165 4422 Planarity : 0.004 0.035 4806 Dihedral : 5.073 59.335 4491 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.25 % Allowed : 13.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3343 helix: 2.87 (0.20), residues: 636 sheet: 0.98 (0.16), residues: 952 loop : -0.46 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 436 HIS 0.006 0.001 HIS C1064 PHE 0.021 0.002 PHE C 374 TYR 0.033 0.001 TYR C 756 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 30) link_NAG-ASN : angle 1.72968 ( 90) link_BETA1-4 : bond 0.00299 ( 9) link_BETA1-4 : angle 1.54489 ( 27) hydrogen bonds : bond 0.04972 ( 1138) hydrogen bonds : angle 5.13355 ( 3162) SS BOND : bond 0.00689 ( 42) SS BOND : angle 1.34716 ( 84) covalent geometry : bond 0.00396 (27809) covalent geometry : angle 0.57080 (37805) *********************** 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 332 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8229 (t0) cc_final: 0.7623 (t0) REVERT: A 87 ARG cc_start: 0.7917 (mpp80) cc_final: 0.7695 (mpp80) REVERT: B 17 ASP cc_start: 0.8726 (m-30) cc_final: 0.8429 (p0) REVERT: C 170 TYR cc_start: 0.8129 (t80) cc_final: 0.7775 (t80) REVERT: C 189 LEU cc_start: 0.8925 (pp) cc_final: 0.8612 (tp) REVERT: C 314 GLN cc_start: 0.9018 (tt0) cc_final: 0.8655 (tm-30) REVERT: C 421 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: C 424 LYS cc_start: 0.0357 (OUTLIER) cc_final: 0.0120 (ptmt) REVERT: C 512 VAL cc_start: 0.8410 (t) cc_final: 0.8140 (m) REVERT: C 533 LEU cc_start: 0.8974 (tp) cc_final: 0.8640 (mt) REVERT: C 565 PHE cc_start: 0.7785 (m-80) cc_final: 0.7584 (m-10) REVERT: C 581 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8731 (p) REVERT: C 979 ASP cc_start: 0.8461 (t70) cc_final: 0.8145 (t0) REVERT: C 1029 MET cc_start: 0.9568 (tpp) cc_final: 0.9182 (tpp) REVERT: D 73 ASP cc_start: 0.8241 (t0) cc_final: 0.7337 (t0) REVERT: D 82 GLN cc_start: 0.8541 (tp40) cc_final: 0.7779 (tp40) REVERT: D 89 GLU cc_start: 0.8717 (pm20) cc_final: 0.8449 (pm20) REVERT: E 17 ASP cc_start: 0.8676 (m-30) cc_final: 0.8217 (p0) REVERT: F 189 LEU cc_start: 0.9123 (pp) cc_final: 0.8672 (tp) REVERT: F 200 TYR cc_start: 0.8258 (m-10) cc_final: 0.7987 (m-10) REVERT: F 201 PHE cc_start: 0.8318 (t80) cc_final: 0.7987 (t80) REVERT: F 314 GLN cc_start: 0.9017 (tt0) cc_final: 0.8706 (tm-30) REVERT: F 377 PHE cc_start: 0.8765 (t80) cc_final: 0.8514 (t80) REVERT: F 421 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: F 512 VAL cc_start: 0.8498 (t) cc_final: 0.8208 (m) REVERT: F 559 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8094 (t80) REVERT: F 581 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8788 (p) REVERT: F 988 GLU cc_start: 0.8614 (mp0) cc_final: 0.8370 (mp0) REVERT: I 30 ASP cc_start: 0.9144 (p0) cc_final: 0.8934 (p0) REVERT: I 73 ASP cc_start: 0.8230 (t0) cc_final: 0.7428 (t0) REVERT: I 89 GLU cc_start: 0.9047 (mp0) cc_final: 0.8791 (pm20) REVERT: J 105 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.4303 (tm-30) REVERT: K 34 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6639 (mmp80) REVERT: K 170 TYR cc_start: 0.8172 (t80) cc_final: 0.7825 (t80) REVERT: K 189 LEU cc_start: 0.9161 (pp) cc_final: 0.8757 (tp) REVERT: K 314 GLN cc_start: 0.8978 (tt0) cc_final: 0.8562 (tm-30) REVERT: K 512 VAL cc_start: 0.8475 (t) cc_final: 0.8197 (m) REVERT: K 532 ASN cc_start: 0.9274 (t0) cc_final: 0.9022 (t0) REVERT: K 559 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.8011 (t80) REVERT: K 894 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9273 (mt) REVERT: K 979 ASP cc_start: 0.8586 (t0) cc_final: 0.8265 (t0) REVERT: K 988 GLU cc_start: 0.8680 (mp0) cc_final: 0.8267 (mp0) outliers start: 67 outliers final: 39 residues processed: 319 average time/residue: 1.2722 time to fit residues: 482.7476 Evaluate side-chains 297 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 2.799 ------------------------------------------------------------------------------- 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 A residue 67 ARG 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 130 VAL 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 421 TYR 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 581 THR 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 85 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 127 VAL 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 421 TYR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 453 TYR 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 33 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 105 GLU Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 130 VAL 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 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 894 LEU Chi-restraints excluded: chain K residue 916 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 205 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 270 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 3 GLN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.114668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.066552 restraints weight = 55172.935| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.70 r_work: 0.2825 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27890 Z= 0.110 Angle : 0.552 10.598 38006 Z= 0.279 Chirality : 0.043 0.167 4422 Planarity : 0.003 0.034 4806 Dihedral : 4.899 57.606 4491 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.46 % Allowed : 13.29 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3343 helix: 3.10 (0.20), residues: 635 sheet: 0.96 (0.16), residues: 981 loop : -0.44 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 436 HIS 0.003 0.001 HIS E 91 PHE 0.019 0.001 PHE F 400 TYR 0.044 0.001 TYR F 265 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 30) link_NAG-ASN : angle 1.54316 ( 90) link_BETA1-4 : bond 0.00404 ( 9) link_BETA1-4 : angle 1.41561 ( 27) hydrogen bonds : bond 0.04350 ( 1138) hydrogen bonds : angle 4.93344 ( 3162) SS BOND : bond 0.00415 ( 42) SS BOND : angle 1.14173 ( 84) covalent geometry : bond 0.00246 (27809) covalent geometry : angle 0.54487 (37805) *********************** 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: 73 poor density : 274 time to evaluate : 2.787 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 73 ASP cc_start: 0.7993 (t0) cc_final: 0.7196 (t0) REVERT: A 87 ARG cc_start: 0.7839 (mpp80) cc_final: 0.7527 (mpp80) REVERT: B 17 ASP cc_start: 0.8716 (m-30) cc_final: 0.8499 (OUTLIER) REVERT: C 170 TYR cc_start: 0.8159 (t80) cc_final: 0.7681 (t80) REVERT: C 189 LEU cc_start: 0.8936 (pp) cc_final: 0.8594 (tp) REVERT: C 229 LEU cc_start: 0.8885 (mm) cc_final: 0.8569 (mt) REVERT: C 314 GLN cc_start: 0.8977 (tt0) cc_final: 0.8577 (tm-30) REVERT: C 421 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: C 512 VAL cc_start: 0.8327 (t) cc_final: 0.8066 (m) REVERT: C 533 LEU cc_start: 0.8967 (tp) cc_final: 0.8496 (mt) REVERT: C 559 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7967 (t80) REVERT: C 565 PHE cc_start: 0.7704 (m-80) cc_final: 0.7486 (m-10) REVERT: C 581 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8679 (p) REVERT: C 979 ASP cc_start: 0.8417 (t70) cc_final: 0.8101 (t0) REVERT: C 1029 MET cc_start: 0.9483 (tpp) cc_final: 0.9046 (tpp) REVERT: D 16 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.7727 (mpp80) REVERT: D 73 ASP cc_start: 0.7963 (t0) cc_final: 0.7023 (t0) REVERT: D 82 GLN cc_start: 0.8279 (tp40) cc_final: 0.7534 (tp40) REVERT: D 87 ARG cc_start: 0.8014 (mpt-90) cc_final: 0.7662 (mtt-85) REVERT: D 89 GLU cc_start: 0.8646 (pm20) cc_final: 0.8357 (pm20) REVERT: E 17 ASP cc_start: 0.8602 (m-30) cc_final: 0.8207 (p0) REVERT: F 189 LEU cc_start: 0.9131 (pp) cc_final: 0.8668 (tp) REVERT: F 200 TYR cc_start: 0.8193 (m-10) cc_final: 0.7915 (m-10) REVERT: F 201 PHE cc_start: 0.8270 (t80) cc_final: 0.7999 (t80) REVERT: F 314 GLN cc_start: 0.8969 (tt0) cc_final: 0.8627 (tm-30) REVERT: F 377 PHE cc_start: 0.8798 (t80) cc_final: 0.8471 (t80) REVERT: F 512 VAL cc_start: 0.8395 (t) cc_final: 0.8121 (m) REVERT: F 559 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7975 (t80) REVERT: F 581 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8758 (p) REVERT: F 988 GLU cc_start: 0.8604 (mp0) cc_final: 0.8295 (mp0) REVERT: I 16 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7679 (mpp80) REVERT: I 30 ASP cc_start: 0.9037 (p0) cc_final: 0.8830 (p0) REVERT: I 67 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7790 (mtm180) REVERT: I 73 ASP cc_start: 0.8013 (t0) cc_final: 0.7189 (t0) REVERT: I 87 ARG cc_start: 0.8123 (mpp80) cc_final: 0.7339 (mpp80) REVERT: I 89 GLU cc_start: 0.9075 (mp0) cc_final: 0.8787 (pm20) REVERT: J 24 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7629 (mtp-110) REVERT: J 105 GLU cc_start: 0.4644 (OUTLIER) cc_final: 0.4255 (tm-30) REVERT: K 170 TYR cc_start: 0.8126 (t80) cc_final: 0.7739 (t80) REVERT: K 189 LEU cc_start: 0.9153 (pp) cc_final: 0.8745 (tp) REVERT: K 314 GLN cc_start: 0.8874 (tt0) cc_final: 0.8480 (tm-30) REVERT: K 377 PHE cc_start: 0.8501 (t80) cc_final: 0.8288 (t80) REVERT: K 512 VAL cc_start: 0.8382 (t) cc_final: 0.8104 (m) REVERT: K 532 ASN cc_start: 0.9284 (t0) cc_final: 0.9026 (t0) REVERT: K 894 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9178 (mt) REVERT: K 979 ASP cc_start: 0.8580 (t0) cc_final: 0.8219 (t0) REVERT: K 988 GLU cc_start: 0.8653 (mp0) cc_final: 0.8213 (mp0) outliers start: 73 outliers final: 42 residues processed: 335 average time/residue: 1.2531 time to fit residues: 497.3277 Evaluate side-chains 302 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 2.919 ------------------------------------------------------------------------------- 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 A residue 67 ARG 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 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR 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 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 118 THR 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 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 559 PHE Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 979 ASP 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 121 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 105 GLU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 130 VAL 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 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 894 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 332 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 205 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 295 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.112556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063379 restraints weight = 55055.492| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.75 r_work: 0.2753 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27890 Z= 0.169 Angle : 0.580 10.216 38006 Z= 0.294 Chirality : 0.044 0.177 4422 Planarity : 0.004 0.033 4806 Dihedral : 4.954 58.876 4491 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.25 % Allowed : 13.79 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3343 helix: 2.99 (0.20), residues: 634 sheet: 0.93 (0.16), residues: 958 loop : -0.45 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 436 HIS 0.006 0.001 HIS C1064 PHE 0.027 0.002 PHE F 92 TYR 0.036 0.001 TYR K 756 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 30) link_NAG-ASN : angle 1.61855 ( 90) link_BETA1-4 : bond 0.00289 ( 9) link_BETA1-4 : angle 1.50612 ( 27) hydrogen bonds : bond 0.04881 ( 1138) hydrogen bonds : angle 4.99875 ( 3162) SS BOND : bond 0.00521 ( 42) SS BOND : angle 1.23219 ( 84) covalent geometry : bond 0.00402 (27809) covalent geometry : angle 0.57147 (37805) *********************** 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 334 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 267 time to evaluate : 2.923 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 73 ASP cc_start: 0.7935 (t0) cc_final: 0.7075 (t0) REVERT: A 76 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8818 (mtmm) REVERT: B 17 ASP cc_start: 0.8681 (m-30) cc_final: 0.8423 (OUTLIER) REVERT: C 170 TYR cc_start: 0.8261 (t80) cc_final: 0.7838 (t80) REVERT: C 189 LEU cc_start: 0.8924 (pp) cc_final: 0.8557 (tp) REVERT: C 229 LEU cc_start: 0.8876 (mm) cc_final: 0.8562 (mt) REVERT: C 314 GLN cc_start: 0.8985 (tt0) cc_final: 0.8523 (tm-30) REVERT: C 421 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: C 512 VAL cc_start: 0.8316 (t) cc_final: 0.8056 (m) REVERT: C 533 LEU cc_start: 0.8910 (tp) cc_final: 0.8511 (mt) REVERT: C 565 PHE cc_start: 0.7702 (m-80) cc_final: 0.7496 (m-10) REVERT: C 581 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8625 (p) REVERT: C 979 ASP cc_start: 0.8398 (t70) cc_final: 0.8063 (t0) REVERT: C 1029 MET cc_start: 0.9372 (tpp) cc_final: 0.9017 (tpp) REVERT: D 16 ARG cc_start: 0.8363 (tpp-160) cc_final: 0.7731 (mpp80) REVERT: D 73 ASP cc_start: 0.7911 (t0) cc_final: 0.6959 (t0) REVERT: D 82 GLN cc_start: 0.8206 (tp40) cc_final: 0.7871 (tp40) REVERT: D 87 ARG cc_start: 0.8026 (mpt-90) cc_final: 0.7720 (mtt-85) REVERT: D 89 GLU cc_start: 0.8638 (pm20) cc_final: 0.8326 (pm20) REVERT: E 17 ASP cc_start: 0.8619 (m-30) cc_final: 0.8189 (p0) REVERT: F 189 LEU cc_start: 0.9099 (pp) cc_final: 0.8690 (tp) REVERT: F 200 TYR cc_start: 0.8209 (m-10) cc_final: 0.7951 (m-10) REVERT: F 201 PHE cc_start: 0.8261 (t80) cc_final: 0.8005 (t80) REVERT: F 314 GLN cc_start: 0.8978 (tt0) cc_final: 0.8561 (tm-30) REVERT: F 377 PHE cc_start: 0.8766 (t80) cc_final: 0.8545 (t80) REVERT: F 512 VAL cc_start: 0.8353 (t) cc_final: 0.8080 (m) REVERT: F 559 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7872 (t80) REVERT: F 581 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8713 (p) REVERT: F 988 GLU cc_start: 0.8545 (mp0) cc_final: 0.8220 (mp0) REVERT: I 30 ASP cc_start: 0.9053 (p0) cc_final: 0.8845 (p0) REVERT: I 67 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8108 (mtm180) REVERT: I 73 ASP cc_start: 0.7941 (t0) cc_final: 0.7156 (t0) REVERT: I 76 LYS cc_start: 0.9192 (mttp) cc_final: 0.8901 (ttmm) REVERT: I 89 GLU cc_start: 0.9081 (mp0) cc_final: 0.8794 (pm20) REVERT: J 17 ASP cc_start: 0.8897 (m-30) cc_final: 0.8508 (p0) REVERT: J 24 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7644 (mtp-110) REVERT: J 107 LYS cc_start: 0.5391 (tptp) cc_final: 0.5187 (mttm) REVERT: K 170 TYR cc_start: 0.8196 (t80) cc_final: 0.7821 (t80) REVERT: K 189 LEU cc_start: 0.9149 (pp) cc_final: 0.8721 (tp) REVERT: K 314 GLN cc_start: 0.8875 (tt0) cc_final: 0.8416 (tm-30) REVERT: K 377 PHE cc_start: 0.8582 (t80) cc_final: 0.8321 (t80) REVERT: K 512 VAL cc_start: 0.8380 (t) cc_final: 0.8105 (m) REVERT: K 532 ASN cc_start: 0.9292 (t0) cc_final: 0.9037 (t0) REVERT: K 894 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9154 (mt) REVERT: K 979 ASP cc_start: 0.8530 (t0) cc_final: 0.8189 (t0) REVERT: K 988 GLU cc_start: 0.8547 (mp0) cc_final: 0.8117 (mp0) outliers start: 67 outliers final: 39 residues processed: 321 average time/residue: 1.2097 time to fit residues: 462.5192 Evaluate side-chains 297 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 76 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 368 LEU Chi-restraints excluded: chain C residue 421 TYR 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 581 THR 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 D residue 118 THR 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 267 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 453 TYR 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 121 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 130 VAL 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 433 VAL Chi-restraints excluded: chain K residue 453 TYR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 916 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 95 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 540 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.113377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064414 restraints weight = 54962.321| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.76 r_work: 0.2819 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3588 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= 0.126 Angle : 0.570 10.294 38006 Z= 0.288 Chirality : 0.043 0.175 4422 Planarity : 0.004 0.033 4806 Dihedral : 4.891 57.712 4491 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.75 % Allowed : 14.67 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3343 helix: 3.09 (0.20), residues: 635 sheet: 0.87 (0.15), residues: 1023 loop : -0.40 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP K 436 HIS 0.004 0.001 HIS C1064 PHE 0.027 0.001 PHE F 92 TYR 0.038 0.001 TYR K 756 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 30) link_NAG-ASN : angle 1.50806 ( 90) link_BETA1-4 : bond 0.00358 ( 9) link_BETA1-4 : angle 1.41358 ( 27) hydrogen bonds : bond 0.04471 ( 1138) hydrogen bonds : angle 4.89059 ( 3162) SS BOND : bond 0.00500 ( 42) SS BOND : angle 1.14416 ( 84) covalent geometry : bond 0.00289 (27809) covalent geometry : angle 0.56322 (37805) *********************** 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 320 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 2.877 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 16 ARG cc_start: 0.8237 (tpp-160) cc_final: 0.7574 (mpp80) REVERT: A 73 ASP cc_start: 0.7902 (t0) cc_final: 0.7079 (t0) REVERT: A 87 ARG cc_start: 0.7722 (mpp80) cc_final: 0.7461 (mpp80) REVERT: B 17 ASP cc_start: 0.8701 (m-30) cc_final: 0.8465 (OUTLIER) REVERT: C 170 TYR cc_start: 0.8232 (t80) cc_final: 0.7745 (t80) REVERT: C 189 LEU cc_start: 0.8924 (pp) cc_final: 0.8548 (tp) REVERT: C 229 LEU cc_start: 0.8872 (mm) cc_final: 0.8554 (mt) REVERT: C 314 GLN cc_start: 0.8968 (tt0) cc_final: 0.8511 (tm-30) REVERT: C 421 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6694 (m-80) REVERT: C 512 VAL cc_start: 0.8326 (t) cc_final: 0.8064 (m) REVERT: C 533 LEU cc_start: 0.8852 (tp) cc_final: 0.8557 (mt) REVERT: C 581 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8631 (p) REVERT: C 979 ASP cc_start: 0.8376 (t70) cc_final: 0.8070 (t0) REVERT: C 1029 MET cc_start: 0.9375 (tpp) cc_final: 0.8992 (tpp) REVERT: D 16 ARG cc_start: 0.8370 (tpp-160) cc_final: 0.7752 (mpp80) REVERT: D 73 ASP cc_start: 0.7874 (t0) cc_final: 0.6910 (t0) REVERT: D 82 GLN cc_start: 0.8206 (tp40) cc_final: 0.7449 (tp40) REVERT: D 87 ARG cc_start: 0.8015 (mpt-90) cc_final: 0.7745 (mpt-90) REVERT: D 89 GLU cc_start: 0.8592 (pm20) cc_final: 0.8298 (pm20) REVERT: E 17 ASP cc_start: 0.8618 (m-30) cc_final: 0.8235 (p0) REVERT: F 189 LEU cc_start: 0.9108 (pp) cc_final: 0.8663 (tp) REVERT: F 200 TYR cc_start: 0.8203 (m-10) cc_final: 0.7917 (m-10) REVERT: F 201 PHE cc_start: 0.8264 (t80) cc_final: 0.8038 (t80) REVERT: F 314 GLN cc_start: 0.8963 (tt0) cc_final: 0.8575 (tm-30) REVERT: F 353 TRP cc_start: 0.8352 (p-90) cc_final: 0.8015 (p-90) REVERT: F 377 PHE cc_start: 0.8806 (t80) cc_final: 0.8571 (t80) REVERT: F 512 VAL cc_start: 0.8279 (t) cc_final: 0.7997 (m) REVERT: F 559 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7896 (t80) REVERT: F 581 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8705 (p) REVERT: F 988 GLU cc_start: 0.8567 (mp0) cc_final: 0.8191 (mp0) REVERT: I 16 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7708 (mpp80) REVERT: I 30 ASP cc_start: 0.9023 (p0) cc_final: 0.8810 (p0) REVERT: I 67 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8098 (mtm180) REVERT: I 73 ASP cc_start: 0.7878 (t0) cc_final: 0.7095 (t0) REVERT: I 76 LYS cc_start: 0.9189 (mttp) cc_final: 0.8891 (ttmm) REVERT: I 89 GLU cc_start: 0.9089 (mp0) cc_final: 0.8794 (pm20) REVERT: J 17 ASP cc_start: 0.8938 (m-30) cc_final: 0.8624 (p0) REVERT: J 24 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7564 (mtp-110) REVERT: J 107 LYS cc_start: 0.5474 (tptp) cc_final: 0.5033 (mtpp) REVERT: K 170 TYR cc_start: 0.8186 (t80) cc_final: 0.7755 (t80) REVERT: K 189 LEU cc_start: 0.9119 (pp) cc_final: 0.8641 (tp) REVERT: K 314 GLN cc_start: 0.8849 (tt0) cc_final: 0.8406 (tm-30) REVERT: K 512 VAL cc_start: 0.8379 (t) cc_final: 0.8106 (m) REVERT: K 532 ASN cc_start: 0.9265 (t0) cc_final: 0.8982 (t0) REVERT: K 894 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9132 (mt) REVERT: K 979 ASP cc_start: 0.8538 (t0) cc_final: 0.8177 (t0) REVERT: K 988 GLU cc_start: 0.8551 (mp0) cc_final: 0.8112 (mp0) outliers start: 52 outliers final: 40 residues processed: 313 average time/residue: 1.4559 time to fit residues: 543.9452 Evaluate side-chains 297 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 3.019 ------------------------------------------------------------------------------- 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 A residue 67 ARG 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 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR 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 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 D residue 118 THR 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 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 F residue 581 THR Chi-restraints excluded: chain F residue 979 ASP 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 121 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 130 VAL 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 894 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 312 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 299 optimal weight: 0.4980 chunk 10 optimal weight: 0.0470 overall best weight: 1.5084 ------------------------------------------------------------------------------- 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 3 GLN J 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.112483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.063140 restraints weight = 55168.210| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.70 r_work: 0.2780 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27890 Z= 0.168 Angle : 0.590 10.035 38006 Z= 0.300 Chirality : 0.044 0.190 4422 Planarity : 0.004 0.034 4806 Dihedral : 4.940 58.663 4491 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.55 % Allowed : 14.83 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3343 helix: 2.97 (0.20), residues: 637 sheet: 0.83 (0.16), residues: 977 loop : -0.47 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 353 HIS 0.006 0.001 HIS C1064 PHE 0.025 0.002 PHE F 92 TYR 0.036 0.001 TYR K 756 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 30) link_NAG-ASN : angle 1.56842 ( 90) link_BETA1-4 : bond 0.00280 ( 9) link_BETA1-4 : angle 1.47699 ( 27) hydrogen bonds : bond 0.04847 ( 1138) hydrogen bonds : angle 4.96610 ( 3162) SS BOND : bond 0.00518 ( 42) SS BOND : angle 1.17535 ( 84) covalent geometry : bond 0.00401 (27809) covalent geometry : angle 0.58227 (37805) ********************** 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 309 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 2.982 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 16 ARG cc_start: 0.8301 (tpp-160) cc_final: 0.7742 (mpp80) REVERT: A 73 ASP cc_start: 0.8017 (t0) cc_final: 0.7192 (t0) REVERT: A 87 ARG cc_start: 0.7858 (mpp80) cc_final: 0.7579 (mpp80) REVERT: B 17 ASP cc_start: 0.8743 (m-30) cc_final: 0.8410 (p0) REVERT: C 170 TYR cc_start: 0.8337 (t80) cc_final: 0.7975 (t80) REVERT: C 189 LEU cc_start: 0.8919 (pp) cc_final: 0.8522 (tp) REVERT: C 229 LEU cc_start: 0.8903 (mm) cc_final: 0.8611 (mt) REVERT: C 314 GLN cc_start: 0.8985 (tt0) cc_final: 0.8542 (tm-30) REVERT: C 421 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: C 512 VAL cc_start: 0.8423 (t) cc_final: 0.8171 (m) REVERT: C 533 LEU cc_start: 0.8826 (tp) cc_final: 0.8495 (mt) REVERT: C 581 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8658 (p) REVERT: C 979 ASP cc_start: 0.8391 (t70) cc_final: 0.8066 (t0) REVERT: C 1029 MET cc_start: 0.9372 (tpp) cc_final: 0.9021 (tpp) REVERT: D 16 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.7794 (mpp80) REVERT: D 73 ASP cc_start: 0.8000 (t0) cc_final: 0.7028 (t0) REVERT: D 89 GLU cc_start: 0.8659 (pm20) cc_final: 0.8421 (pm20) REVERT: E 17 ASP cc_start: 0.8660 (m-30) cc_final: 0.8217 (OUTLIER) REVERT: E 107 LYS cc_start: 0.5535 (tptp) cc_final: 0.5325 (tppt) REVERT: F 189 LEU cc_start: 0.9109 (pp) cc_final: 0.8695 (tp) REVERT: F 200 TYR cc_start: 0.8212 (m-10) cc_final: 0.7947 (m-10) REVERT: F 201 PHE cc_start: 0.8301 (t80) cc_final: 0.8058 (t80) REVERT: F 314 GLN cc_start: 0.9007 (tt0) cc_final: 0.8611 (tm-30) REVERT: F 353 TRP cc_start: 0.8388 (p-90) cc_final: 0.8098 (p-90) REVERT: F 512 VAL cc_start: 0.8333 (t) cc_final: 0.7997 (m) REVERT: F 559 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7964 (t80) REVERT: F 581 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8659 (p) REVERT: F 988 GLU cc_start: 0.8557 (mp0) cc_final: 0.8184 (mp0) REVERT: I 16 ARG cc_start: 0.8339 (tpp-160) cc_final: 0.7812 (mpp80) REVERT: I 30 ASP cc_start: 0.9084 (p0) cc_final: 0.8870 (p0) REVERT: I 67 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8162 (mtm180) REVERT: I 73 ASP cc_start: 0.8013 (t0) cc_final: 0.7234 (t0) REVERT: I 76 LYS cc_start: 0.9220 (mttp) cc_final: 0.8922 (ttmm) REVERT: I 89 GLU cc_start: 0.9095 (mp0) cc_final: 0.8810 (pm20) REVERT: J 17 ASP cc_start: 0.8917 (m-30) cc_final: 0.8581 (p0) REVERT: J 79 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7278 (mm-30) REVERT: J 105 GLU cc_start: 0.4537 (tm-30) cc_final: 0.4316 (tm-30) REVERT: J 107 LYS cc_start: 0.5603 (tptp) cc_final: 0.5260 (mtpp) REVERT: K 170 TYR cc_start: 0.8277 (t80) cc_final: 0.7885 (t80) REVERT: K 189 LEU cc_start: 0.9095 (pp) cc_final: 0.8555 (tp) REVERT: K 314 GLN cc_start: 0.8889 (tt0) cc_final: 0.8467 (tm-30) REVERT: K 512 VAL cc_start: 0.8407 (t) cc_final: 0.8142 (m) REVERT: K 532 ASN cc_start: 0.9254 (t0) cc_final: 0.8970 (t0) REVERT: K 564 GLN cc_start: 0.7620 (tt0) cc_final: 0.7130 (mt0) REVERT: K 894 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9184 (mt) REVERT: K 979 ASP cc_start: 0.8529 (t0) cc_final: 0.8190 (t0) REVERT: K 988 GLU cc_start: 0.8543 (mp0) cc_final: 0.8116 (mp0) outliers start: 46 outliers final: 40 residues processed: 303 average time/residue: 1.2835 time to fit residues: 459.2018 Evaluate side-chains 301 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 2.801 ------------------------------------------------------------------------------- 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 A residue 67 ARG 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 368 LEU Chi-restraints excluded: chain C residue 421 TYR 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 581 THR 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 D residue 118 THR 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 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 F residue 581 THR Chi-restraints excluded: chain F residue 979 ASP 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 121 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 130 VAL 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 855 PHE Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 142 optimal weight: 0.0670 chunk 146 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 322 optimal weight: 0.0770 chunk 153 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.113105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.063902 restraints weight = 55150.787| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.70 r_work: 0.2796 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27890 Z= 0.130 Angle : 0.578 10.632 38006 Z= 0.294 Chirality : 0.044 0.181 4422 Planarity : 0.004 0.033 4806 Dihedral : 4.888 57.794 4491 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.58 % Allowed : 15.00 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3343 helix: 2.99 (0.20), residues: 643 sheet: 0.83 (0.16), residues: 991 loop : -0.45 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 353 HIS 0.004 0.001 HIS C1064 PHE 0.026 0.001 PHE F 92 TYR 0.038 0.001 TYR K 756 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 30) link_NAG-ASN : angle 1.49921 ( 90) link_BETA1-4 : bond 0.00352 ( 9) link_BETA1-4 : angle 1.40680 ( 27) hydrogen bonds : bond 0.04535 ( 1138) hydrogen bonds : angle 4.88504 ( 3162) SS BOND : bond 0.00463 ( 42) SS BOND : angle 1.06431 ( 84) covalent geometry : bond 0.00303 (27809) covalent geometry : angle 0.57187 (37805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30655.30 seconds wall clock time: 529 minutes 50.05 seconds (31790.05 seconds total)