Starting phenix.real_space_refine on Mon Aug 25 15:40:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7chh_30374/08_2025/7chh_30374.cif Found real_map, /net/cci-nas-00/data/ceres_data/7chh_30374/08_2025/7chh_30374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7chh_30374/08_2025/7chh_30374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7chh_30374/08_2025/7chh_30374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7chh_30374/08_2025/7chh_30374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7chh_30374/08_2025/7chh_30374.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18430 2.51 5 N 4798 2.21 5 O 5672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 231 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29029 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7734 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 52, 'TRANS': 950} Chain breaks: 10 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 7652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7652 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 53, 'TRANS': 940} Chain breaks: 10 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7672 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 945} Chain breaks: 10 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 3, 'TYR:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "G" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "H" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "J" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "F" 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: "I" 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: "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: "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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.95, per 1000 atoms: 0.20 Number of scatterers: 29029 At special positions: 0 Unit cell: (136.68, 152.76, 227.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5672 8.00 N 4798 7.00 C 18430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 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=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 93 " 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 F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1310 " - " ASN B1134 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B1074 " " NAG C1301 " - " ASN C1134 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 801 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 616 " " NAG C1311 " - " ASN C 603 " " NAG C1313 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG I 1 " - " ASN B 717 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C 717 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6854 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 59 sheets defined 20.5% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.692A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.999A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.741A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.913A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 881 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.877A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.054A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.910A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.195A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.564A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.815A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.599A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.534A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.641A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.569A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.657A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.566A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.987A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.024A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.776A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 390' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.821A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.812A 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 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.513A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.829A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.029A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.781A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.958A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 84 through 88 removed outlier: 3.959A pdb=" N VAL H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 84 through 88 removed outlier: 3.959A pdb=" N VAL K 88 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 7.866A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.026A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.769A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.880A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.260A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.721A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.757A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.029A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.029A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.343A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.519A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.880A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.345A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 172 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.785A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE B 392 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.730A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.772A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.772A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 691 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.547A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.539A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.692A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.519A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.830A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.720A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.504A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.051A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.364A pdb=" N PHE C 392 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.688A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 723 removed outlier: 6.837A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 723 removed outlier: 6.837A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.460A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF3, first strand: chain 'D' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.506A pdb=" N THR D 119 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 95 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS E 23 " --> pdb=" O PHE E 76 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 76 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP E 75 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 72 " --> pdb=" O ASP E 75 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY E 89 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 41 " --> pdb=" O TYR E 92 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU E 51 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR E 54 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU G 20 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.505A pdb=" N THR G 119 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR G 95 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS H 23 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE H 76 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP H 75 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER H 72 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR H 41 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU H 42 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU H 51 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR H 54 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN H 58 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU J 20 " --> pdb=" O LEU J 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.506A pdb=" N THR J 119 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR J 95 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL J 37 " --> pdb=" O TYR J 95 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS K 23 " --> pdb=" O PHE K 76 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE K 76 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP K 75 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER K 72 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY K 89 " --> pdb=" O LEU K 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR K 41 " --> pdb=" O TYR K 92 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU K 42 " --> pdb=" O LEU K 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU K 51 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR K 54 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN K 58 " --> pdb=" O TYR K 54 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 2931 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: 6.23 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 9318 1.35 - 1.48: 8012 1.48 - 1.62: 12165 1.62 - 1.75: 2 1.75 - 1.89: 163 Bond restraints: 29660 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.86e+00 bond pdb=" CA TRP J 109 " pdb=" C TRP J 109 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.72e-02 3.38e+03 8.16e+00 bond pdb=" CB ARG D 43 " pdb=" CG ARG D 43 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.87e+00 bond pdb=" CB ARG J 43 " pdb=" CG ARG J 43 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.81e+00 ... (remaining 29655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 39507 3.13 - 6.26: 710 6.26 - 9.39: 107 9.39 - 12.51: 32 12.51 - 15.64: 11 Bond angle restraints: 40367 Sorted by residual: angle pdb=" CB ARG G 100 " pdb=" CG ARG G 100 " pdb=" CD ARG G 100 " ideal model delta sigma weight residual 111.30 95.66 15.64 2.30e+00 1.89e-01 4.63e+01 angle pdb=" CB ARG J 100 " pdb=" CG ARG J 100 " pdb=" CD ARG J 100 " ideal model delta sigma weight residual 111.30 95.67 15.63 2.30e+00 1.89e-01 4.62e+01 angle pdb=" CB ARG D 100 " pdb=" CG ARG D 100 " pdb=" CD ARG D 100 " ideal model delta sigma weight residual 111.30 95.72 15.58 2.30e+00 1.89e-01 4.59e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 128.88 -14.48 2.30e+00 1.89e-01 3.96e+01 angle pdb=" C ASN A 165 " pdb=" N CYS A 166 " pdb=" CA CYS A 166 " ideal model delta sigma weight residual 122.74 111.32 11.42 1.82e+00 3.02e-01 3.94e+01 ... (remaining 40362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 16673 21.99 - 43.98: 1213 43.98 - 65.98: 213 65.98 - 87.97: 39 87.97 - 109.96: 5 Dihedral angle restraints: 18143 sinusoidal: 7454 harmonic: 10689 Sorted by residual: dihedral pdb=" CA LEU B 293 " pdb=" C LEU B 293 " pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta harmonic sigma weight residual -180.00 -117.24 -62.76 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.81 -85.19 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 177.64 -84.64 1 1.00e+01 1.00e-02 8.70e+01 ... (remaining 18140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3924 0.082 - 0.164: 689 0.164 - 0.246: 61 0.246 - 0.327: 10 0.327 - 0.409: 10 Chirality restraints: 4694 Sorted by residual: chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CB ILE C 666 " pdb=" CA ILE C 666 " pdb=" CG1 ILE C 666 " pdb=" CG2 ILE C 666 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C2 NAG C1308 " pdb=" C1 NAG C1308 " pdb=" C3 NAG C1308 " pdb=" N2 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 4691 not shown) Planarity restraints: 5215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 29 " 0.025 2.00e-02 2.50e+03 3.54e-02 2.19e+01 pdb=" CG PHE J 29 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE J 29 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE J 29 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE J 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE J 29 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE J 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 29 " -0.025 2.00e-02 2.50e+03 3.53e-02 2.18e+01 pdb=" CG PHE D 29 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE D 29 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE D 29 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE D 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 29 " -0.025 2.00e-02 2.50e+03 3.51e-02 2.16e+01 pdb=" CG PHE G 29 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE G 29 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE G 29 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE G 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 29 " -0.000 2.00e-02 2.50e+03 ... (remaining 5212 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1627 2.73 - 3.27: 26607 3.27 - 3.81: 47275 3.81 - 4.36: 54094 4.36 - 4.90: 95682 Nonbonded interactions: 225285 Sorted by model distance: nonbonded pdb=" O GLY D 116 " pdb=" OG SER E 48 " model vdw 2.182 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 2.253 3.120 nonbonded pdb=" O SER D 85 " pdb=" OG SER D 85 " model vdw 2.257 3.040 nonbonded pdb=" O SER G 85 " pdb=" OG SER G 85 " model vdw 2.257 3.040 nonbonded pdb=" O SER J 85 " pdb=" OG SER J 85 " model vdw 2.257 3.040 ... (remaining 225280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 95 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA or n \ ame C or name O or name CB )) or resid 130 through 140 or (resid 157 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or resid 217 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 243 or resid 264 through 516 or resid 521 through 620 or resid 641 t \ hrough 1311)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 or (resid 239 and (n \ ame N or name CA or name C or name O or name CB )) or resid 240 through 289 or ( \ resid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 328 or resid 334 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 th \ rough 1313)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 66 or resid 81 throug \ h 95 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 104 or (resid 105 and (name N or name CA or name C o \ r name O or name CB )) or resid 106 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 209 \ or resid 217 through 243 or resid 264 through 328 or resid 334 through 516 or re \ sid 521 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.770 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.050 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0174 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 : 0.007 0.109 29741 Z= 0.319 Angle : 1.125 15.643 40566 Z= 0.594 Chirality : 0.063 0.409 4694 Planarity : 0.007 0.085 5183 Dihedral : 15.259 109.961 11157 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 3.56 % Allowed : 1.19 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.12), residues: 3626 helix: -1.01 (0.18), residues: 665 sheet: -0.57 (0.17), residues: 843 loop : -1.85 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.002 ARG C 466 TYR 0.038 0.003 TYR C 423 PHE 0.080 0.004 PHE J 29 TRP 0.030 0.004 TRP C 353 HIS 0.013 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00726 (29660) covalent geometry : angle 1.10335 (40367) SS BOND : bond 0.01091 ( 44) SS BOND : angle 2.83893 ( 88) hydrogen bonds : bond 0.22590 ( 1048) hydrogen bonds : angle 9.29396 ( 2931) link_BETA1-4 : bond 0.01057 ( 5) link_BETA1-4 : angle 2.91849 ( 15) link_NAG-ASN : bond 0.00687 ( 32) link_NAG-ASN : angle 3.82195 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 233 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1151 (m-80) cc_final: 0.0766 (m-80) REVERT: A 618 THR cc_start: 0.0081 (m) cc_final: -0.0947 (p) REVERT: A 823 PHE cc_start: 0.0703 (m-10) cc_final: -0.2136 (p90) REVERT: A 1029 MET cc_start: 0.0721 (tpp) cc_final: -0.0307 (tpp) REVERT: A 1110 TYR cc_start: 0.0702 (t80) cc_final: -0.0291 (t80) REVERT: B 206 LYS cc_start: 0.1404 (tttt) cc_final: 0.0928 (tttm) REVERT: B 614 ASP cc_start: -0.0604 (p0) cc_final: -0.0839 (t0) REVERT: B 1014 ARG cc_start: 0.2351 (ttm110) cc_final: 0.0877 (tpt170) REVERT: B 1115 ILE cc_start: 0.2112 (mt) cc_final: 0.1518 (pt) REVERT: E 94 MET cc_start: -0.4673 (ttp) cc_final: -0.4910 (ttp) REVERT: G 4 LEU cc_start: -0.0684 (OUTLIER) cc_final: -0.1404 (mm) REVERT: G 34 MET cc_start: 0.0140 (OUTLIER) cc_final: -0.0384 (tpp) REVERT: G 52 SER cc_start: 0.1959 (OUTLIER) cc_final: 0.1476 (m) REVERT: G 53 ASP cc_start: 0.0272 (OUTLIER) cc_final: -0.0624 (m-30) REVERT: H 41 TYR cc_start: -0.0516 (OUTLIER) cc_final: -0.1300 (m-80) REVERT: H 76 PHE cc_start: 0.0814 (OUTLIER) cc_final: -0.0256 (m-10) REVERT: H 111 ILE cc_start: -0.0088 (OUTLIER) cc_final: -0.0453 (tt) REVERT: J 52 SER cc_start: -0.0323 (OUTLIER) cc_final: -0.0803 (p) REVERT: J 105 TYR cc_start: -0.3500 (m-80) cc_final: -0.3789 (m-80) REVERT: J 108 VAL cc_start: -0.0478 (OUTLIER) cc_final: -0.0699 (p) REVERT: K 11 LEU cc_start: -0.2711 (OUTLIER) cc_final: -0.2954 (tp) REVERT: K 41 TYR cc_start: 0.0873 (OUTLIER) cc_final: -0.0082 (m-80) outliers start: 111 outliers final: 28 residues processed: 338 average time/residue: 0.1674 time to fit residues: 91.0039 Evaluate side-chains 173 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 41 TYR Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 PHE Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 41 TYR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 76 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 965 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 563 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1048 HIS C 901 GLN C 954 GLN C1010 GLN C1106 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.302463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5289 r_free = 0.5289 target = 0.295356 restraints weight = 67135.358| |-----------------------------------------------------------------------------| r_work (start): 0.5283 rms_B_bonded: 1.34 r_work: 0.5183 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.5183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0467 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29741 Z= 0.146 Angle : 0.697 13.236 40566 Z= 0.351 Chirality : 0.047 0.450 4694 Planarity : 0.005 0.089 5183 Dihedral : 8.386 104.403 4901 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 1.44 % Allowed : 7.74 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.13), residues: 3626 helix: 0.33 (0.20), residues: 659 sheet: -0.38 (0.17), residues: 878 loop : -1.52 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 19 TYR 0.042 0.002 TYR B 204 PHE 0.023 0.002 PHE B 238 TRP 0.024 0.002 TRP J 47 HIS 0.007 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00315 (29660) covalent geometry : angle 0.67790 (40367) SS BOND : bond 0.00478 ( 44) SS BOND : angle 1.60532 ( 88) hydrogen bonds : bond 0.04497 ( 1048) hydrogen bonds : angle 6.30987 ( 2931) link_BETA1-4 : bond 0.00406 ( 5) link_BETA1-4 : angle 1.86894 ( 15) link_NAG-ASN : bond 0.00770 ( 32) link_NAG-ASN : angle 3.05859 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.0984 (m-80) cc_final: 0.0580 (m-80) REVERT: A 618 THR cc_start: 0.0884 (m) cc_final: -0.0492 (p) REVERT: A 823 PHE cc_start: 0.1728 (m-10) cc_final: 0.0300 (m-80) REVERT: A 1110 TYR cc_start: 0.1549 (t80) cc_final: 0.0208 (t80) REVERT: B 614 ASP cc_start: -0.0050 (p0) cc_final: -0.0294 (t0) REVERT: B 1014 ARG cc_start: 0.2540 (ttm110) cc_final: 0.0699 (tpp-160) REVERT: C 355 ARG cc_start: 0.0013 (OUTLIER) cc_final: -0.2689 (ptt180) REVERT: C 1089 PHE cc_start: 0.3368 (m-80) cc_final: 0.2761 (m-80) REVERT: C 1111 GLU cc_start: 0.0303 (tt0) cc_final: -0.0299 (mm-30) REVERT: E 94 MET cc_start: -0.2695 (ttp) cc_final: -0.3044 (ttp) REVERT: H 54 TYR cc_start: 0.1210 (OUTLIER) cc_final: 0.0309 (p90) REVERT: J 105 TYR cc_start: -0.2040 (m-80) cc_final: -0.2891 (m-80) REVERT: K 26 SER cc_start: 0.0593 (OUTLIER) cc_final: -0.0618 (t) REVERT: K 102 THR cc_start: 0.1074 (OUTLIER) cc_final: 0.0423 (p) outliers start: 45 outliers final: 19 residues processed: 191 average time/residue: 0.2059 time to fit residues: 63.3544 Evaluate side-chains 149 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 292 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 177 optimal weight: 0.7980 chunk 351 optimal weight: 40.0000 chunk 321 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 259 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 388 ASN B 901 GLN B 913 GLN B 949 GLN B 957 GLN B1101 HIS ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.300949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 170)---------------| | r_work = 0.5267 r_free = 0.5267 target = 0.292385 restraints weight = 65893.592| |-----------------------------------------------------------------------------| r_work (start): 0.5262 rms_B_bonded: 1.36 r_work: 0.5162 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.5162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0898 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 29741 Z= 0.183 Angle : 0.748 13.060 40566 Z= 0.376 Chirality : 0.049 0.279 4694 Planarity : 0.006 0.117 5183 Dihedral : 7.655 98.073 4840 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 2.25 % Allowed : 10.82 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.13), residues: 3626 helix: 0.06 (0.20), residues: 662 sheet: -0.39 (0.17), residues: 891 loop : -1.44 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1039 TYR 0.026 0.002 TYR A1067 PHE 0.028 0.002 PHE A 718 TRP 0.021 0.002 TRP J 109 HIS 0.012 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00403 (29660) covalent geometry : angle 0.73213 (40367) SS BOND : bond 0.00665 ( 44) SS BOND : angle 1.47837 ( 88) hydrogen bonds : bond 0.05024 ( 1048) hydrogen bonds : angle 6.30378 ( 2931) link_BETA1-4 : bond 0.00920 ( 5) link_BETA1-4 : angle 2.11725 ( 15) link_NAG-ASN : bond 0.00933 ( 32) link_NAG-ASN : angle 2.83146 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 145 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2593 (OUTLIER) cc_final: 0.1491 (m) REVERT: A 451 TYR cc_start: 0.1226 (m-80) cc_final: 0.0831 (m-80) REVERT: A 714 ILE cc_start: -0.1677 (OUTLIER) cc_final: -0.1953 (pt) REVERT: A 740 MET cc_start: 0.1067 (tpt) cc_final: 0.0788 (tpt) REVERT: A 853 GLN cc_start: 0.5364 (tm-30) cc_final: 0.3317 (mm110) REVERT: A 990 GLU cc_start: 0.5481 (OUTLIER) cc_final: 0.4672 (tt0) REVERT: A 1110 TYR cc_start: 0.3212 (t80) cc_final: 0.1299 (t80) REVERT: A 1130 ILE cc_start: -0.0034 (OUTLIER) cc_final: -0.0522 (mt) REVERT: B 1014 ARG cc_start: 0.2976 (ttm110) cc_final: 0.0823 (tpp-160) REVERT: B 1040 VAL cc_start: -0.0390 (OUTLIER) cc_final: -0.1115 (t) REVERT: C 300 LYS cc_start: 0.2139 (ttmt) cc_final: 0.1572 (mmtm) REVERT: C 355 ARG cc_start: -0.0503 (OUTLIER) cc_final: -0.3063 (ptt180) REVERT: C 1089 PHE cc_start: 0.3905 (m-80) cc_final: 0.2911 (m-80) REVERT: C 1106 GLN cc_start: 0.1630 (OUTLIER) cc_final: 0.1269 (mp10) REVERT: C 1111 GLU cc_start: 0.0626 (tt0) cc_final: 0.0005 (mm-30) REVERT: D 36 TRP cc_start: 0.0499 (m100) cc_final: 0.0037 (m100) REVERT: E 94 MET cc_start: -0.2959 (ttp) cc_final: -0.3168 (ttp) REVERT: G 34 MET cc_start: 0.1809 (tpp) cc_final: 0.1464 (tpp) REVERT: K 26 SER cc_start: 0.0626 (OUTLIER) cc_final: -0.0578 (t) REVERT: K 102 THR cc_start: 0.1676 (m) cc_final: 0.1022 (p) outliers start: 70 outliers final: 24 residues processed: 200 average time/residue: 0.1916 time to fit residues: 63.0461 Evaluate side-chains 157 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 348 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 212 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 228 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 258 optimal weight: 40.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 901 GLN B1064 HIS C 580 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.300686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 156)---------------| | r_work = 0.5262 r_free = 0.5262 target = 0.291675 restraints weight = 65939.019| |-----------------------------------------------------------------------------| r_work (start): 0.5258 rms_B_bonded: 1.38 r_work: 0.5163 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.5163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0919 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29741 Z= 0.131 Angle : 0.633 10.807 40566 Z= 0.316 Chirality : 0.046 0.279 4694 Planarity : 0.005 0.085 5183 Dihedral : 6.936 95.537 4828 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 1.89 % Allowed : 13.16 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.13), residues: 3626 helix: 0.55 (0.20), residues: 645 sheet: -0.45 (0.17), residues: 942 loop : -1.39 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 100 TYR 0.018 0.001 TYR C1067 PHE 0.026 0.001 PHE C 377 TRP 0.011 0.001 TRP C 353 HIS 0.020 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00285 (29660) covalent geometry : angle 0.61481 (40367) SS BOND : bond 0.00554 ( 44) SS BOND : angle 1.59460 ( 88) hydrogen bonds : bond 0.04103 ( 1048) hydrogen bonds : angle 5.87247 ( 2931) link_BETA1-4 : bond 0.00725 ( 5) link_BETA1-4 : angle 1.94114 ( 15) link_NAG-ASN : bond 0.00610 ( 32) link_NAG-ASN : angle 2.73830 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1261 (m-80) cc_final: 0.0766 (m-80) REVERT: A 779 GLN cc_start: 0.0189 (OUTLIER) cc_final: -0.0429 (mt0) REVERT: A 853 GLN cc_start: 0.5417 (tm-30) cc_final: 0.3503 (mm110) REVERT: A 898 PHE cc_start: 0.0367 (t80) cc_final: 0.0030 (t80) REVERT: A 1110 TYR cc_start: 0.3368 (t80) cc_final: 0.1480 (t80) REVERT: B 53 ASP cc_start: 0.1058 (OUTLIER) cc_final: 0.0545 (t70) REVERT: B 714 ILE cc_start: -0.1470 (OUTLIER) cc_final: -0.2237 (mt) REVERT: B 797 PHE cc_start: 0.2854 (m-10) cc_final: 0.1781 (m-80) REVERT: B 916 LEU cc_start: 0.0620 (OUTLIER) cc_final: -0.1911 (mp) REVERT: B 1040 VAL cc_start: -0.0045 (OUTLIER) cc_final: -0.0668 (t) REVERT: C 300 LYS cc_start: 0.2189 (ttmt) cc_final: 0.1608 (mmtt) REVERT: C 355 ARG cc_start: -0.0477 (OUTLIER) cc_final: -0.2863 (ptt180) REVERT: C 1081 ILE cc_start: 0.1849 (mm) cc_final: 0.1634 (mm) REVERT: C 1089 PHE cc_start: 0.3379 (m-80) cc_final: 0.2359 (m-80) REVERT: C 1111 GLU cc_start: 0.0653 (tt0) cc_final: 0.0094 (mm-30) REVERT: J 100 ARG cc_start: 0.1503 (OUTLIER) cc_final: -0.0956 (ptt-90) REVERT: K 26 SER cc_start: 0.1042 (OUTLIER) cc_final: -0.0019 (t) REVERT: K 102 THR cc_start: 0.1910 (m) cc_final: 0.1274 (p) outliers start: 59 outliers final: 27 residues processed: 176 average time/residue: 0.2000 time to fit residues: 57.6230 Evaluate side-chains 154 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 312 optimal weight: 50.0000 chunk 93 optimal weight: 0.5980 chunk 10 optimal weight: 40.0000 chunk 114 optimal weight: 0.9980 chunk 325 optimal weight: 50.0000 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 258 optimal weight: 40.0000 chunk 309 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1036 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.299645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 175)---------------| | r_work = 0.5253 r_free = 0.5253 target = 0.290304 restraints weight = 65745.407| |-----------------------------------------------------------------------------| r_work (start): 0.5252 rms_B_bonded: 1.42 r_work: 0.5155 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.5155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0999 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 29741 Z= 0.128 Angle : 0.627 11.227 40566 Z= 0.311 Chirality : 0.045 0.275 4694 Planarity : 0.005 0.080 5183 Dihedral : 6.630 91.365 4828 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.05 % Allowed : 14.25 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3626 helix: 0.73 (0.21), residues: 641 sheet: -0.43 (0.17), residues: 940 loop : -1.32 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 38 TYR 0.026 0.001 TYR B 204 PHE 0.016 0.001 PHE A 800 TRP 0.013 0.001 TRP D 36 HIS 0.037 0.002 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00283 (29660) covalent geometry : angle 0.61029 (40367) SS BOND : bond 0.00375 ( 44) SS BOND : angle 1.24256 ( 88) hydrogen bonds : bond 0.03977 ( 1048) hydrogen bonds : angle 5.72417 ( 2931) link_BETA1-4 : bond 0.00596 ( 5) link_BETA1-4 : angle 2.07116 ( 15) link_NAG-ASN : bond 0.00600 ( 32) link_NAG-ASN : angle 2.70595 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 131 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2603 (OUTLIER) cc_final: 0.1477 (m) REVERT: A 317 ASN cc_start: 0.2599 (OUTLIER) cc_final: 0.2382 (m-40) REVERT: A 451 TYR cc_start: 0.1045 (m-80) cc_final: 0.0450 (m-80) REVERT: A 762 GLN cc_start: 0.2479 (mm110) cc_final: 0.1603 (tp40) REVERT: A 779 GLN cc_start: 0.0158 (OUTLIER) cc_final: -0.0635 (mt0) REVERT: A 853 GLN cc_start: 0.5226 (tm-30) cc_final: 0.3374 (mm110) REVERT: A 898 PHE cc_start: 0.0658 (t80) cc_final: 0.0166 (t80) REVERT: A 990 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.4707 (tt0) REVERT: B 714 ILE cc_start: -0.1872 (OUTLIER) cc_final: -0.2686 (mt) REVERT: B 797 PHE cc_start: 0.3169 (m-10) cc_final: 0.2289 (m-80) REVERT: B 916 LEU cc_start: 0.0788 (OUTLIER) cc_final: -0.1821 (mp) REVERT: B 1071 GLN cc_start: 0.3046 (mp10) cc_final: 0.2388 (tt0) REVERT: C 300 LYS cc_start: 0.2241 (ttmt) cc_final: 0.1685 (mmtm) REVERT: C 355 ARG cc_start: -0.0685 (OUTLIER) cc_final: -0.2895 (ptt-90) REVERT: C 1081 ILE cc_start: 0.2222 (mm) cc_final: 0.2021 (mm) REVERT: C 1089 PHE cc_start: 0.3209 (m-80) cc_final: 0.2196 (m-80) REVERT: G 34 MET cc_start: 0.1516 (tpp) cc_final: 0.1137 (tpp) REVERT: K 26 SER cc_start: 0.0460 (OUTLIER) cc_final: -0.0299 (t) REVERT: K 31 HIS cc_start: 0.3730 (OUTLIER) cc_final: 0.3499 (m-70) REVERT: K 95 GLN cc_start: 0.2166 (pp30) cc_final: 0.0942 (mm-40) outliers start: 64 outliers final: 28 residues processed: 184 average time/residue: 0.1854 time to fit residues: 56.6522 Evaluate side-chains 160 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 202 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 358 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 804 GLN B 901 GLN B1106 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN K 31 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.299265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.290808 restraints weight = 65732.917| |-----------------------------------------------------------------------------| r_work (start): 0.5255 rms_B_bonded: 1.44 r_work: 0.5146 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.5146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1073 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29741 Z= 0.133 Angle : 0.637 11.164 40566 Z= 0.314 Chirality : 0.046 0.512 4694 Planarity : 0.005 0.077 5183 Dihedral : 7.053 99.712 4828 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.47 % Allowed : 14.80 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.14), residues: 3626 helix: 0.78 (0.21), residues: 636 sheet: -0.30 (0.17), residues: 914 loop : -1.36 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 100 TYR 0.021 0.001 TYR B 37 PHE 0.027 0.002 PHE C 377 TRP 0.015 0.001 TRP J 109 HIS 0.021 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00290 (29660) covalent geometry : angle 0.61978 (40367) SS BOND : bond 0.00433 ( 44) SS BOND : angle 1.22598 ( 88) hydrogen bonds : bond 0.04009 ( 1048) hydrogen bonds : angle 5.67589 ( 2931) link_BETA1-4 : bond 0.00666 ( 5) link_BETA1-4 : angle 2.18871 ( 15) link_NAG-ASN : bond 0.00567 ( 32) link_NAG-ASN : angle 2.78220 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 133 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2538 (OUTLIER) cc_final: 0.1185 (m) REVERT: A 400 PHE cc_start: 0.2052 (OUTLIER) cc_final: 0.1651 (p90) REVERT: A 451 TYR cc_start: 0.0928 (m-80) cc_final: 0.0309 (m-80) REVERT: A 562 PHE cc_start: 0.2729 (p90) cc_final: 0.1884 (p90) REVERT: A 731 MET cc_start: 0.1106 (OUTLIER) cc_final: 0.0634 (ppp) REVERT: A 762 GLN cc_start: 0.2375 (mm-40) cc_final: 0.1468 (tp40) REVERT: A 779 GLN cc_start: 0.0259 (OUTLIER) cc_final: -0.0722 (mt0) REVERT: A 853 GLN cc_start: 0.5325 (tm-30) cc_final: 0.3665 (mm110) REVERT: A 898 PHE cc_start: 0.1015 (t80) cc_final: 0.0498 (t80) REVERT: A 1130 ILE cc_start: 0.0275 (OUTLIER) cc_final: -0.0153 (mt) REVERT: B 313 TYR cc_start: 0.2660 (m-80) cc_final: 0.0607 (t80) REVERT: B 670 ILE cc_start: 0.1367 (OUTLIER) cc_final: 0.0840 (pt) REVERT: B 714 ILE cc_start: -0.1888 (OUTLIER) cc_final: -0.2584 (mt) REVERT: B 797 PHE cc_start: 0.3016 (m-10) cc_final: 0.2265 (m-80) REVERT: B 916 LEU cc_start: 0.0903 (OUTLIER) cc_final: -0.1754 (mp) REVERT: B 959 LEU cc_start: -0.1543 (OUTLIER) cc_final: -0.1756 (mm) REVERT: B 1071 GLN cc_start: 0.3375 (mp10) cc_final: 0.2388 (tt0) REVERT: C 300 LYS cc_start: 0.2029 (ttmt) cc_final: 0.1565 (mmtt) REVERT: C 364 ASP cc_start: 0.2092 (t0) cc_final: 0.1258 (p0) REVERT: C 1089 PHE cc_start: 0.3203 (m-80) cc_final: 0.2102 (m-80) REVERT: G 34 MET cc_start: 0.1537 (tpp) cc_final: 0.1127 (tpp) REVERT: K 26 SER cc_start: 0.0526 (OUTLIER) cc_final: -0.0282 (t) outliers start: 77 outliers final: 39 residues processed: 194 average time/residue: 0.1772 time to fit residues: 57.9996 Evaluate side-chains 171 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 342 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 907 ASN B1058 HIS C 314 GLN C 343 ASN C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.298897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5287 r_free = 0.5287 target = 0.294532 restraints weight = 69197.368| |-----------------------------------------------------------------------------| r_work (start): 0.5283 rms_B_bonded: 0.77 r_work: 0.5218 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.5177 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.5177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1344 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 29741 Z= 0.217 Angle : 0.810 18.912 40566 Z= 0.400 Chirality : 0.051 0.455 4694 Planarity : 0.006 0.083 5183 Dihedral : 8.009 123.902 4828 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.86 % Allowed : 15.38 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.13), residues: 3626 helix: 0.17 (0.21), residues: 620 sheet: -0.67 (0.17), residues: 931 loop : -1.50 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 355 TYR 0.031 0.002 TYR A1067 PHE 0.034 0.002 PHE A1052 TRP 0.030 0.002 TRP J 109 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00494 (29660) covalent geometry : angle 0.78939 (40367) SS BOND : bond 0.00413 ( 44) SS BOND : angle 1.70944 ( 88) hydrogen bonds : bond 0.05228 ( 1048) hydrogen bonds : angle 6.35126 ( 2931) link_BETA1-4 : bond 0.00912 ( 5) link_BETA1-4 : angle 2.61771 ( 15) link_NAG-ASN : bond 0.00736 ( 32) link_NAG-ASN : angle 3.35413 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 143 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2676 (OUTLIER) cc_final: 0.1659 (m) REVERT: A 220 PHE cc_start: 0.0345 (t80) cc_final: -0.0504 (p90) REVERT: A 400 PHE cc_start: 0.2081 (OUTLIER) cc_final: 0.1431 (p90) REVERT: A 451 TYR cc_start: 0.1246 (m-80) cc_final: 0.0606 (m-80) REVERT: A 762 GLN cc_start: 0.3109 (mm-40) cc_final: 0.2082 (tp40) REVERT: A 779 GLN cc_start: 0.0383 (OUTLIER) cc_final: -0.1108 (mt0) REVERT: A 853 GLN cc_start: 0.5492 (tm-30) cc_final: 0.3515 (mm110) REVERT: A 869 MET cc_start: 0.1242 (mtp) cc_final: -0.0167 (tpp) REVERT: A 898 PHE cc_start: 0.1786 (t80) cc_final: 0.1202 (t80) REVERT: A 1091 ARG cc_start: 0.3567 (mtp85) cc_final: 0.2609 (mpt-90) REVERT: B 189 LEU cc_start: 0.2360 (OUTLIER) cc_final: 0.1975 (mp) REVERT: B 318 PHE cc_start: -0.0032 (OUTLIER) cc_final: -0.1073 (p90) REVERT: B 386 LYS cc_start: -0.0270 (ptpt) cc_final: -0.0643 (ttmt) REVERT: B 670 ILE cc_start: 0.1828 (OUTLIER) cc_final: 0.1553 (tt) REVERT: B 714 ILE cc_start: -0.1634 (OUTLIER) cc_final: -0.2352 (mt) REVERT: B 797 PHE cc_start: 0.3453 (m-10) cc_final: 0.2676 (m-80) REVERT: B 909 ILE cc_start: -0.0635 (OUTLIER) cc_final: -0.1459 (pt) REVERT: B 916 LEU cc_start: 0.1170 (OUTLIER) cc_final: -0.1469 (mp) REVERT: B 1058 HIS cc_start: 0.1391 (OUTLIER) cc_final: 0.0747 (m-70) REVERT: C 300 LYS cc_start: 0.2547 (ttmt) cc_final: 0.2089 (mptt) REVERT: C 1089 PHE cc_start: 0.3745 (m-80) cc_final: 0.2699 (m-80) REVERT: G 34 MET cc_start: 0.1618 (tpp) cc_final: 0.1196 (tpp) REVERT: K 26 SER cc_start: 0.1505 (OUTLIER) cc_final: 0.0268 (t) REVERT: K 95 GLN cc_start: 0.2422 (pp30) cc_final: 0.1258 (mm-40) REVERT: K 102 THR cc_start: 0.1932 (OUTLIER) cc_final: 0.0864 (p) outliers start: 89 outliers final: 54 residues processed: 215 average time/residue: 0.1781 time to fit residues: 64.0393 Evaluate side-chains 195 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 129 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1052 PHE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 284 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 148 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 34 optimal weight: 40.0000 chunk 241 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 190 optimal weight: 0.0060 chunk 276 optimal weight: 9.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.299044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.294519 restraints weight = 69124.513| |-----------------------------------------------------------------------------| r_work (start): 0.5287 rms_B_bonded: 0.83 r_work: 0.5213 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.5172 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.5172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1337 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 29741 Z= 0.160 Angle : 0.702 11.349 40566 Z= 0.347 Chirality : 0.048 0.391 4694 Planarity : 0.005 0.076 5183 Dihedral : 7.355 111.569 4828 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.44 % Allowed : 16.12 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.13), residues: 3626 helix: 0.26 (0.21), residues: 626 sheet: -0.63 (0.17), residues: 900 loop : -1.43 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 905 TYR 0.023 0.001 TYR A 380 PHE 0.028 0.002 PHE C 377 TRP 0.020 0.002 TRP J 109 HIS 0.029 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00356 (29660) covalent geometry : angle 0.68385 (40367) SS BOND : bond 0.00376 ( 44) SS BOND : angle 1.31553 ( 88) hydrogen bonds : bond 0.04566 ( 1048) hydrogen bonds : angle 6.11433 ( 2931) link_BETA1-4 : bond 0.00439 ( 5) link_BETA1-4 : angle 2.81693 ( 15) link_NAG-ASN : bond 0.00677 ( 32) link_NAG-ASN : angle 2.93134 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 140 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.0304 (t80) cc_final: -0.0222 (p90) REVERT: A 400 PHE cc_start: 0.2180 (OUTLIER) cc_final: 0.1525 (p90) REVERT: A 451 TYR cc_start: 0.1119 (m-80) cc_final: 0.0433 (m-80) REVERT: A 762 GLN cc_start: 0.3619 (mm-40) cc_final: 0.2198 (tp40) REVERT: A 779 GLN cc_start: 0.0456 (OUTLIER) cc_final: -0.1020 (mt0) REVERT: A 853 GLN cc_start: 0.5142 (tm-30) cc_final: 0.3497 (mm110) REVERT: A 898 PHE cc_start: 0.2011 (t80) cc_final: 0.1482 (t80) REVERT: A 1029 MET cc_start: -0.0562 (ttt) cc_final: -0.1591 (mtp) REVERT: A 1091 ARG cc_start: 0.3485 (mtp85) cc_final: 0.3243 (mmt90) REVERT: B 386 LYS cc_start: -0.0426 (ptpt) cc_final: -0.0721 (ttmt) REVERT: B 670 ILE cc_start: 0.1756 (OUTLIER) cc_final: 0.1189 (tp) REVERT: B 714 ILE cc_start: -0.1683 (OUTLIER) cc_final: -0.2507 (mt) REVERT: B 797 PHE cc_start: 0.3694 (m-10) cc_final: 0.2955 (m-80) REVERT: B 916 LEU cc_start: 0.1213 (OUTLIER) cc_final: -0.1429 (mp) REVERT: B 1071 GLN cc_start: 0.4681 (mp10) cc_final: 0.2588 (tt0) REVERT: C 36 VAL cc_start: 0.0121 (OUTLIER) cc_final: -0.0129 (p) REVERT: C 223 LEU cc_start: 0.0587 (tp) cc_final: 0.0168 (mt) REVERT: C 300 LYS cc_start: 0.2592 (ttmt) cc_final: 0.2115 (mmtt) REVERT: C 364 ASP cc_start: 0.2253 (t0) cc_final: 0.1316 (p0) REVERT: C 784 GLN cc_start: 0.0480 (mt0) cc_final: 0.0026 (pt0) REVERT: C 988 GLU cc_start: 0.0151 (OUTLIER) cc_final: -0.0396 (mm-30) REVERT: C 1089 PHE cc_start: 0.3656 (m-80) cc_final: 0.2348 (m-80) REVERT: G 34 MET cc_start: 0.1407 (tpp) cc_final: 0.1042 (tpp) REVERT: K 4 MET cc_start: 0.3895 (pmm) cc_final: 0.3370 (ptp) REVERT: K 26 SER cc_start: 0.1553 (OUTLIER) cc_final: 0.0345 (t) REVERT: K 95 GLN cc_start: 0.2571 (pp30) cc_final: 0.1809 (mp10) REVERT: K 102 THR cc_start: 0.1335 (OUTLIER) cc_final: -0.0845 (p) outliers start: 76 outliers final: 53 residues processed: 204 average time/residue: 0.1833 time to fit residues: 62.2297 Evaluate side-chains 192 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 130 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 171 optimal weight: 0.0000 chunk 223 optimal weight: 0.9990 chunk 302 optimal weight: 0.0170 chunk 3 optimal weight: 0.9990 chunk 343 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 257 optimal weight: 0.9990 chunk 244 optimal weight: 50.0000 chunk 225 optimal weight: 7.9990 chunk 365 optimal weight: 0.9980 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN A1058 HIS C 965 GLN D 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.299352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 135)---------------| | r_work = 0.5255 r_free = 0.5255 target = 0.290663 restraints weight = 65388.593| |-----------------------------------------------------------------------------| r_work (start): 0.5250 rms_B_bonded: 1.39 r_work: 0.5150 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.5150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1192 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29741 Z= 0.113 Angle : 0.614 10.884 40566 Z= 0.302 Chirality : 0.045 0.411 4694 Planarity : 0.004 0.070 5183 Dihedral : 6.783 112.256 4828 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.80 % Allowed : 16.92 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.14), residues: 3626 helix: 0.67 (0.21), residues: 626 sheet: -0.54 (0.17), residues: 920 loop : -1.30 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 328 TYR 0.043 0.001 TYR B 351 PHE 0.033 0.001 PHE B 306 TRP 0.017 0.001 TRP D 36 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00244 (29660) covalent geometry : angle 0.59606 (40367) SS BOND : bond 0.00314 ( 44) SS BOND : angle 1.12628 ( 88) hydrogen bonds : bond 0.03888 ( 1048) hydrogen bonds : angle 5.67635 ( 2931) link_BETA1-4 : bond 0.00435 ( 5) link_BETA1-4 : angle 3.01481 ( 15) link_NAG-ASN : bond 0.00561 ( 32) link_NAG-ASN : angle 2.71433 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 136 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2381 (OUTLIER) cc_final: 0.1264 (m) REVERT: A 64 TRP cc_start: 0.4267 (t60) cc_final: 0.3624 (t60) REVERT: A 220 PHE cc_start: 0.0202 (t80) cc_final: -0.0283 (p90) REVERT: A 278 LYS cc_start: 0.1940 (tmtt) cc_final: 0.1546 (mmtt) REVERT: A 400 PHE cc_start: 0.2102 (OUTLIER) cc_final: 0.1411 (p90) REVERT: A 451 TYR cc_start: 0.0920 (m-80) cc_final: 0.0134 (m-80) REVERT: A 581 THR cc_start: 0.1574 (OUTLIER) cc_final: 0.1288 (m) REVERT: A 614 ASP cc_start: 0.5333 (t70) cc_final: 0.3825 (p0) REVERT: A 762 GLN cc_start: 0.3597 (mm-40) cc_final: 0.2133 (tp40) REVERT: A 779 GLN cc_start: 0.0017 (OUTLIER) cc_final: -0.0704 (mt0) REVERT: A 853 GLN cc_start: 0.5033 (tm-30) cc_final: 0.3470 (mm110) REVERT: A 898 PHE cc_start: 0.1750 (t80) cc_final: 0.1346 (t80) REVERT: A 1029 MET cc_start: -0.0392 (ttt) cc_final: -0.1256 (mtp) REVERT: B 670 ILE cc_start: 0.1544 (OUTLIER) cc_final: 0.1140 (tp) REVERT: B 690 GLN cc_start: 0.2229 (OUTLIER) cc_final: 0.1998 (mm110) REVERT: B 697 MET cc_start: 0.0326 (mtt) cc_final: -0.2556 (mtm) REVERT: B 714 ILE cc_start: -0.1803 (OUTLIER) cc_final: -0.2494 (mt) REVERT: B 797 PHE cc_start: 0.3429 (m-10) cc_final: 0.2757 (m-80) REVERT: B 905 ARG cc_start: -0.0514 (OUTLIER) cc_final: -0.0966 (mtt-85) REVERT: B 916 LEU cc_start: 0.1116 (OUTLIER) cc_final: -0.1436 (mp) REVERT: B 1071 GLN cc_start: 0.4586 (mp10) cc_final: 0.2658 (tt0) REVERT: B 1109 PHE cc_start: 0.2106 (t80) cc_final: 0.1148 (t80) REVERT: C 241 LEU cc_start: 0.3313 (mm) cc_final: 0.2697 (mm) REVERT: C 300 LYS cc_start: 0.2577 (ttmt) cc_final: 0.2109 (mmtt) REVERT: C 364 ASP cc_start: 0.2118 (t0) cc_final: 0.1200 (p0) REVERT: C 784 GLN cc_start: 0.0354 (mt0) cc_final: 0.0010 (pt0) REVERT: C 988 GLU cc_start: -0.0048 (OUTLIER) cc_final: -0.0513 (mm-30) REVERT: C 1089 PHE cc_start: 0.3365 (m-80) cc_final: 0.2289 (m-80) REVERT: G 34 MET cc_start: 0.2134 (tpp) cc_final: 0.1713 (tpp) REVERT: K 4 MET cc_start: 0.4094 (pmm) cc_final: 0.3729 (ptp) REVERT: K 26 SER cc_start: 0.0981 (OUTLIER) cc_final: -0.0178 (t) REVERT: K 95 GLN cc_start: 0.1711 (pp30) cc_final: 0.1492 (pm20) outliers start: 56 outliers final: 38 residues processed: 181 average time/residue: 0.1770 time to fit residues: 53.0619 Evaluate side-chains 177 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 125 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 949 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.298006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5308 r_free = 0.5308 target = 0.296316 restraints weight = 69373.064| |-----------------------------------------------------------------------------| r_work (start): 0.5310 rms_B_bonded: 0.32 r_work: 0.5269 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.5232 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.5232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1446 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.216 29741 Z= 0.266 Angle : 0.942 24.164 40566 Z= 0.470 Chirality : 0.056 0.379 4694 Planarity : 0.007 0.087 5183 Dihedral : 8.028 100.613 4828 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.42 % Favored : 92.55 % Rotamer: Outliers : 2.15 % Allowed : 16.79 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.13), residues: 3626 helix: -0.43 (0.20), residues: 615 sheet: -0.78 (0.17), residues: 865 loop : -1.65 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 38 TYR 0.034 0.002 TYR A1067 PHE 0.045 0.003 PHE A1052 TRP 0.045 0.003 TRP D 109 HIS 0.019 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00605 (29660) covalent geometry : angle 0.92295 (40367) SS BOND : bond 0.00433 ( 44) SS BOND : angle 1.75087 ( 88) hydrogen bonds : bond 0.06229 ( 1048) hydrogen bonds : angle 6.94241 ( 2931) link_BETA1-4 : bond 0.00619 ( 5) link_BETA1-4 : angle 3.36963 ( 15) link_NAG-ASN : bond 0.00880 ( 32) link_NAG-ASN : angle 3.47176 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 146 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.5472 (t60) cc_final: 0.4454 (t60) REVERT: A 400 PHE cc_start: 0.1896 (OUTLIER) cc_final: 0.1038 (p90) REVERT: A 451 TYR cc_start: 0.1305 (m-80) cc_final: 0.0722 (m-80) REVERT: A 716 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7419 (p) REVERT: A 779 GLN cc_start: 0.0312 (OUTLIER) cc_final: -0.0839 (mt0) REVERT: A 869 MET cc_start: 0.0616 (mtp) cc_final: -0.0283 (tpp) REVERT: A 990 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.5586 (tt0) REVERT: A 1117 THR cc_start: -0.1661 (m) cc_final: -0.2952 (p) REVERT: B 697 MET cc_start: 0.0244 (mtt) cc_final: -0.3419 (mtp) REVERT: B 714 ILE cc_start: -0.1231 (OUTLIER) cc_final: -0.1766 (mt) REVERT: B 797 PHE cc_start: 0.3784 (m-10) cc_final: 0.2612 (m-80) REVERT: B 800 PHE cc_start: 0.2242 (m-80) cc_final: 0.1499 (m-80) REVERT: B 905 ARG cc_start: 0.1259 (OUTLIER) cc_final: -0.1385 (mtt-85) REVERT: C 126 VAL cc_start: 0.3138 (t) cc_final: 0.2928 (p) REVERT: C 223 LEU cc_start: 0.2081 (tp) cc_final: 0.1657 (mt) REVERT: C 300 LYS cc_start: 0.3148 (ttmt) cc_final: 0.2627 (mmtt) REVERT: C 364 ASP cc_start: 0.1719 (t0) cc_final: 0.0683 (p0) REVERT: C 784 GLN cc_start: 0.0705 (mt0) cc_final: 0.0301 (pt0) REVERT: C 1081 ILE cc_start: 0.3931 (OUTLIER) cc_final: 0.3697 (mm) REVERT: C 1089 PHE cc_start: 0.3955 (m-80) cc_final: 0.3069 (m-80) REVERT: J 109 TRP cc_start: 0.1083 (p90) cc_final: 0.0406 (p90) REVERT: K 4 MET cc_start: 0.4116 (pmm) cc_final: 0.3601 (ptp) outliers start: 67 outliers final: 47 residues processed: 204 average time/residue: 0.1594 time to fit residues: 54.1809 Evaluate side-chains 193 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 189 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 353 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 286 optimal weight: 0.9980 chunk 45 optimal weight: 0.0370 chunk 356 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN B 474 GLN B 774 GLN B 949 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.298387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.288992 restraints weight = 65013.143| |-----------------------------------------------------------------------------| r_work (start): 0.5238 rms_B_bonded: 1.52 r_work: 0.5132 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.5132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1365 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29741 Z= 0.132 Angle : 0.676 13.146 40566 Z= 0.332 Chirality : 0.048 0.601 4694 Planarity : 0.005 0.070 5183 Dihedral : 6.952 100.914 4828 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.41 % Allowed : 17.75 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.13), residues: 3626 helix: 0.21 (0.21), residues: 631 sheet: -0.67 (0.17), residues: 879 loop : -1.44 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.018 0.001 TYR C 351 PHE 0.030 0.001 PHE B 306 TRP 0.022 0.002 TRP D 109 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00284 (29660) covalent geometry : angle 0.65186 (40367) SS BOND : bond 0.00300 ( 44) SS BOND : angle 1.39640 ( 88) hydrogen bonds : bond 0.04375 ( 1048) hydrogen bonds : angle 6.05710 ( 2931) link_BETA1-4 : bond 0.00448 ( 5) link_BETA1-4 : angle 3.37893 ( 15) link_NAG-ASN : bond 0.00729 ( 32) link_NAG-ASN : angle 3.28926 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6169.46 seconds wall clock time: 107 minutes 5.52 seconds (6425.52 seconds total)