Starting phenix.real_space_refine on Mon Sep 14 07:40:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7chh_30374/09_2026/7chh_30374.cif Found real_map, /net/cci-nas-00/data/ceres_data/7chh_30374/09_2026/7chh_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_30374/09_2026/7chh_30374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7chh_30374/09_2026/7chh_30374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7chh_30374/09_2026/7chh_30374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7chh_30374/09_2026/7chh_30374.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7chh_30374/09_2026/7chh_30374.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7chh_30374/09_2026/7chh_30374.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 9 Time building chain proxies: 6.04, per 1000 atoms: 0.21 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: 2.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.36 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: 7.60 Time building geometry restraints manager: 3.47 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 - 17.97: 15419 17.97 - 35.93: 1404 35.93 - 53.90: 378 53.90 - 71.86: 48 71.86 - 89.83: 33 Dihedral angle restraints: 17282 sinusoidal: 6593 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 17279 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.850 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0183 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 : 15.156 89.825 10296 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 are 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/Z covalent geometry : bond 0.00726 / 0.32 (29660) covalent geometry : angle 1.10335 / 0.59 (40367) SS BOND : bond 0.01091 / 0.64 ( 44) SS BOND : angle 2.83893 / 1.83 ( 88) hydrogen bonds : bond 0.22590 / 14.81 ( 1048) hydrogen bonds : angle 9.29396 / 6.38 ( 2931) link_BETA1-4 : bond 0.01057 / 0.53 ( 5) link_BETA1-4 : angle 2.91849 / 1.91 ( 15) link_NAG-ASN : bond 0.00687 / 0.42 ( 32) link_NAG-ASN : angle 3.82195 / 2.95 ( 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 : 0.964 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: -0.0089 (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: 0.1871 time to fit residues: 101.7714 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 : 1.166 ------------------------------------------------------------------------------- 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... 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 C 901 GLN C 954 GLN C1010 GLN C1106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5354 r_free = 0.5354 target = 0.302506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5289 r_free = 0.5289 target = 0.295452 restraints weight = 67189.733| |-----------------------------------------------------------------------------| r_work (start): 0.5283 rms_B_bonded: 1.36 r_work: 0.5189 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.5189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0432 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29741 Z= 0.148 Angle : 0.693 13.549 40566 Z= 0.349 Chirality : 0.047 0.431 4694 Planarity : 0.005 0.088 5183 Dihedral : 6.396 54.486 4040 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.48 % Allowed : 7.51 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 3626 helix: 0.31 (0.20), residues: 665 sheet: -0.38 (0.17), residues: 881 loop : -1.53 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 19 TYR 0.033 0.002 TYR B 204 PHE 0.024 0.002 PHE B 238 TRP 0.025 0.002 TRP J 47 HIS 0.007 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (29660) covalent geometry : angle 0.67404 / 0.34 (40367) SS BOND : bond 0.01367 / 0.82 ( 44) SS BOND : angle 1.59579 / 1.06 ( 88) hydrogen bonds : bond 0.04654 / 3.05 ( 1048) hydrogen bonds : angle 6.40581 / 4.41 ( 2931) link_BETA1-4 : bond 0.00698 / 0.30 ( 5) link_BETA1-4 : angle 1.33339 / 0.88 ( 15) link_NAG-ASN : bond 0.00750 / 0.45 ( 32) link_NAG-ASN : angle 3.05296 / 2.40 ( 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 204 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.0994 (m-80) cc_final: 0.0597 (m-80) REVERT: A 618 THR cc_start: 0.0692 (m) cc_final: -0.0614 (p) REVERT: A 823 PHE cc_start: 0.1673 (m-10) cc_final: -0.1806 (t80) REVERT: A 1029 MET cc_start: 0.0821 (tpp) cc_final: -0.0314 (tpp) REVERT: A 1110 TYR cc_start: 0.1501 (t80) cc_final: 0.0182 (t80) REVERT: B 614 ASP cc_start: -0.0085 (p0) cc_final: -0.0300 (t0) REVERT: B 877 LEU cc_start: 0.3662 (mt) cc_final: 0.3017 (mt) REVERT: B 1014 ARG cc_start: 0.2528 (ttm110) cc_final: 0.0702 (tpp-160) REVERT: C 355 ARG cc_start: -0.0014 (OUTLIER) cc_final: -0.2695 (ptt180) REVERT: C 1089 PHE cc_start: 0.3139 (m-80) cc_final: 0.2689 (m-80) REVERT: C 1111 GLU cc_start: 0.0276 (tt0) cc_final: -0.0341 (mm-30) REVERT: D 48 VAL cc_start: 0.0322 (m) cc_final: 0.0095 (t) REVERT: E 94 MET cc_start: -0.2696 (ttp) cc_final: -0.3056 (ttp) REVERT: G 4 LEU cc_start: 0.0348 (OUTLIER) cc_final: -0.0104 (mt) REVERT: H 54 TYR cc_start: 0.1218 (OUTLIER) cc_final: 0.0352 (p90) REVERT: J 105 TYR cc_start: -0.2155 (m-80) cc_final: -0.2947 (m-80) REVERT: K 26 SER cc_start: 0.0659 (OUTLIER) cc_final: -0.0632 (t) outliers start: 46 outliers final: 21 residues processed: 192 average time/residue: 0.2017 time to fit residues: 62.1325 Evaluate side-chains 156 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 G residue 4 LEU Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 102 THR 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 54 TYR 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: 0.7980 chunk 86 optimal weight: 2.9990 chunk 359 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 351 optimal weight: 50.0000 chunk 321 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 259 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN C 957 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS K 36 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.301940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.5285 r_free = 0.5285 target = 0.294492 restraints weight = 66983.783| |-----------------------------------------------------------------------------| r_work (start): 0.5279 rms_B_bonded: 1.32 r_work: 0.5186 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.5186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0619 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29741 Z= 0.136 Angle : 0.638 13.375 40566 Z= 0.319 Chirality : 0.046 0.274 4694 Planarity : 0.005 0.089 5183 Dihedral : 5.209 45.368 3986 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 1.83 % Allowed : 9.57 % Favored : 88.60 % 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 are not related in a simple way. whole: -1.02 (0.13), residues: 3626 helix: 0.70 (0.20), residues: 655 sheet: -0.29 (0.17), residues: 900 loop : -1.34 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1019 TYR 0.020 0.001 TYR C1067 PHE 0.020 0.002 PHE C1121 TRP 0.020 0.001 TRP J 109 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (29660) covalent geometry : angle 0.62253 / 0.32 (40367) SS BOND : bond 0.00411 / 0.24 ( 44) SS BOND : angle 1.28017 / 0.87 ( 88) hydrogen bonds : bond 0.04250 / 2.81 ( 1048) hydrogen bonds : angle 5.89915 / 4.05 ( 2931) link_BETA1-4 : bond 0.00544 / 0.18 ( 5) link_BETA1-4 : angle 1.48368 / 0.97 ( 15) link_NAG-ASN : bond 0.00691 / 0.45 ( 32) link_NAG-ASN : angle 2.64483 / 2.09 ( 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 201 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1118 (m-80) cc_final: 0.0726 (m-80) REVERT: A 782 PHE cc_start: 0.3719 (m-10) cc_final: 0.2616 (m-10) REVERT: A 898 PHE cc_start: 0.0674 (t80) cc_final: 0.0404 (t80) REVERT: A 1110 TYR cc_start: 0.2200 (t80) cc_final: 0.0541 (t80) REVERT: B 614 ASP cc_start: 0.0027 (p0) cc_final: -0.0245 (t0) REVERT: B 877 LEU cc_start: 0.3562 (mt) cc_final: 0.2847 (mt) REVERT: B 1014 ARG cc_start: 0.2573 (ttm110) cc_final: 0.0556 (ttm-80) REVERT: C 300 LYS cc_start: 0.2127 (ttmt) cc_final: 0.1531 (mmtm) REVERT: C 355 ARG cc_start: -0.0329 (OUTLIER) cc_final: -0.2848 (ptt180) REVERT: C 432 CYS cc_start: 0.1142 (OUTLIER) cc_final: 0.0631 (p) REVERT: C 959 LEU cc_start: 0.2517 (OUTLIER) cc_final: 0.1730 (tp) REVERT: C 1089 PHE cc_start: 0.3558 (m-80) cc_final: 0.2707 (m-80) REVERT: C 1111 GLU cc_start: 0.0301 (tt0) cc_final: -0.0183 (mm-30) REVERT: D 53 ASP cc_start: 0.0335 (OUTLIER) cc_final: 0.0033 (m-30) REVERT: D 95 TYR cc_start: 0.2650 (OUTLIER) cc_final: 0.2183 (p90) REVERT: E 94 MET cc_start: -0.2825 (ttp) cc_final: -0.3059 (ttp) REVERT: G 34 MET cc_start: 0.1502 (tpp) cc_final: 0.1169 (tpp) REVERT: K 26 SER cc_start: 0.0646 (OUTLIER) cc_final: -0.0537 (t) REVERT: K 102 THR cc_start: 0.1537 (m) cc_final: 0.0885 (p) REVERT: K 110 GLU cc_start: 0.1191 (tt0) cc_final: -0.1375 (mp0) outliers start: 57 outliers final: 21 residues processed: 188 average time/residue: 0.1876 time to fit residues: 58.3144 Evaluate side-chains 156 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 592 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 761 THR 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 286 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 959 LEU 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 97 LEU Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 36 ASN 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: 0.4980 chunk 115 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 258 optimal weight: 40.0000 chunk 58 optimal weight: 0.9980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN A1002 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 501 ASN B 901 GLN B 913 GLN B 957 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1064 HIS C 207 HIS ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.299876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 166)---------------| | r_work = 0.5257 r_free = 0.5257 target = 0.290986 restraints weight = 65983.032| |-----------------------------------------------------------------------------| r_work (start): 0.5256 rms_B_bonded: 1.41 r_work: 0.5151 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.5151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0923 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 29741 Z= 0.171 Angle : 0.705 11.876 40566 Z= 0.353 Chirality : 0.048 0.272 4694 Planarity : 0.005 0.101 5183 Dihedral : 5.104 42.468 3968 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 2.15 % Allowed : 12.62 % Favored : 85.23 % 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 are not related in a simple way. whole: -1.19 (0.13), residues: 3626 helix: 0.45 (0.20), residues: 645 sheet: -0.41 (0.17), residues: 889 loop : -1.39 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 466 TYR 0.025 0.002 TYR K 37 PHE 0.023 0.002 PHE A 898 TRP 0.024 0.002 TRP J 109 HIS 0.047 0.002 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (29660) covalent geometry : angle 0.69039 / 0.35 (40367) SS BOND : bond 0.01597 / 0.75 ( 44) SS BOND : angle 1.36077 / 0.90 ( 88) hydrogen bonds : bond 0.04465 / 2.97 ( 1048) hydrogen bonds : angle 6.00356 / 4.12 ( 2931) link_BETA1-4 : bond 0.00589 / 0.23 ( 5) link_BETA1-4 : angle 1.44771 / 0.95 ( 15) link_NAG-ASN : bond 0.00657 / 0.43 ( 32) link_NAG-ASN : angle 2.71207 / 2.16 ( 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 206 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 139 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2694 (OUTLIER) cc_final: 0.1538 (m) REVERT: A 451 TYR cc_start: 0.1209 (m-80) cc_final: 0.0765 (m-80) REVERT: A 714 ILE cc_start: -0.1829 (OUTLIER) cc_final: -0.2232 (pt) REVERT: A 762 GLN cc_start: 0.2357 (mm110) cc_final: 0.1434 (tp40) REVERT: A 779 GLN cc_start: -0.0057 (OUTLIER) cc_final: -0.0749 (mt0) REVERT: A 898 PHE cc_start: 0.1131 (t80) cc_final: 0.0607 (t80) REVERT: A 990 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4574 (tt0) REVERT: A 1110 TYR cc_start: 0.3392 (t80) cc_final: 0.1403 (t80) REVERT: A 1135 ASN cc_start: -0.1851 (OUTLIER) cc_final: -0.2612 (t0) REVERT: B 53 ASP cc_start: 0.1041 (OUTLIER) cc_final: 0.0419 (t70) REVERT: B 421 TYR cc_start: 0.0651 (m-80) cc_final: 0.0430 (m-80) REVERT: B 797 PHE cc_start: 0.2779 (m-10) cc_final: 0.1745 (m-80) REVERT: B 916 LEU cc_start: 0.0365 (OUTLIER) cc_final: -0.2127 (mp) REVERT: B 1040 VAL cc_start: 0.0374 (OUTLIER) cc_final: -0.0194 (t) REVERT: B 1058 HIS cc_start: 0.1025 (OUTLIER) cc_final: 0.0179 (m-70) REVERT: C 300 LYS cc_start: 0.2154 (ttmt) cc_final: 0.1584 (mmtm) REVERT: C 355 ARG cc_start: -0.0052 (OUTLIER) cc_final: -0.2730 (ptt180) REVERT: C 432 CYS cc_start: 0.1002 (OUTLIER) cc_final: 0.0571 (p) REVERT: C 1089 PHE cc_start: 0.3693 (m-80) cc_final: 0.2714 (m-80) REVERT: G 34 MET cc_start: 0.1637 (tpp) cc_final: 0.1175 (tpp) REVERT: K 4 MET cc_start: 0.0125 (tpp) cc_final: -0.1030 (tpp) REVERT: K 26 SER cc_start: 0.0818 (OUTLIER) cc_final: -0.0138 (t) outliers start: 67 outliers final: 26 residues processed: 193 average time/residue: 0.1791 time to fit residues: 56.4605 Evaluate side-chains 160 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 779 GLN 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 1135 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1058 HIS 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 432 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP 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 H residue 70 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 31 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 312 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 114 optimal weight: 0.0000 chunk 325 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 258 optimal weight: 40.0000 chunk 309 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1048 HIS B1058 HIS B1101 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C1036 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.299144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.290805 restraints weight = 66076.390| |-----------------------------------------------------------------------------| r_work (start): 0.5254 rms_B_bonded: 1.42 r_work: 0.5157 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.5157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1033 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 29741 Z= 0.160 Angle : 0.680 12.242 40566 Z= 0.337 Chirality : 0.047 0.282 4694 Planarity : 0.005 0.082 5183 Dihedral : 5.006 40.219 3967 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.34 % Allowed : 14.06 % Favored : 83.60 % 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 are not related in a simple way. whole: -1.21 (0.13), residues: 3626 helix: 0.47 (0.21), residues: 641 sheet: -0.38 (0.17), residues: 887 loop : -1.44 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 38 TYR 0.027 0.002 TYR B 204 PHE 0.029 0.002 PHE C 377 TRP 0.024 0.002 TRP J 109 HIS 0.038 0.002 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (29660) covalent geometry : angle 0.66439 / 0.33 (40367) SS BOND : bond 0.00384 / 0.23 ( 44) SS BOND : angle 1.25393 / 0.82 ( 88) hydrogen bonds : bond 0.04356 / 2.89 ( 1048) hydrogen bonds : angle 5.92626 / 4.07 ( 2931) link_BETA1-4 : bond 0.00813 / 0.36 ( 5) link_BETA1-4 : angle 1.46619 / 0.97 ( 15) link_NAG-ASN : bond 0.00733 / 0.45 ( 32) link_NAG-ASN : angle 2.80890 / 2.22 ( 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 202 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 129 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2655 (OUTLIER) cc_final: 0.1498 (m) REVERT: A 400 PHE cc_start: 0.2162 (OUTLIER) cc_final: 0.1634 (p90) REVERT: A 451 TYR cc_start: 0.1104 (m-80) cc_final: 0.0523 (m-80) REVERT: A 714 ILE cc_start: -0.1428 (OUTLIER) cc_final: -0.2054 (pt) REVERT: A 762 GLN cc_start: 0.2556 (mm-40) cc_final: 0.1703 (tp40) REVERT: A 898 PHE cc_start: 0.1410 (t80) cc_final: 0.0988 (t80) REVERT: B 206 LYS cc_start: 0.1955 (tttt) cc_final: 0.1709 (tttt) REVERT: B 714 ILE cc_start: -0.1687 (OUTLIER) cc_final: -0.2456 (mt) REVERT: B 797 PHE cc_start: 0.3307 (m-10) cc_final: 0.2210 (m-80) REVERT: B 916 LEU cc_start: 0.0635 (OUTLIER) cc_final: -0.1890 (mp) REVERT: C 300 LYS cc_start: 0.2227 (ttmt) cc_final: 0.1724 (mmtm) REVERT: C 355 ARG cc_start: -0.0342 (OUTLIER) cc_final: -0.2863 (ptt180) REVERT: C 432 CYS cc_start: 0.0636 (OUTLIER) cc_final: 0.0215 (p) REVERT: C 1089 PHE cc_start: 0.3299 (m-80) cc_final: 0.2365 (m-80) REVERT: D 94 TYR cc_start: 0.5119 (m-80) cc_final: 0.4894 (m-80) REVERT: G 34 MET cc_start: 0.1390 (tpp) cc_final: 0.1003 (tpp) REVERT: J 105 TYR cc_start: -0.1192 (m-80) cc_final: -0.2042 (m-80) REVERT: K 26 SER cc_start: 0.0862 (OUTLIER) cc_final: -0.0245 (t) outliers start: 73 outliers final: 39 residues processed: 187 average time/residue: 0.1746 time to fit residues: 53.9410 Evaluate side-chains 164 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 592 PHE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 952 VAL 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 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 761 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1007 TYR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 432 CYS 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 1129 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 48 SER Chi-restraints excluded: chain H residue 70 SER 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 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 202 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 358 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 409 GLN B 774 GLN B 804 GLN B 949 GLN B1058 HIS B1106 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN G 74 ASN ** K 95 GLN ** 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 = 0.5334 r_free = 0.5334 target = 0.299731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.295366 restraints weight = 69320.877| |-----------------------------------------------------------------------------| r_work (start): 0.5290 rms_B_bonded: 0.80 r_work: 0.5218 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.5178 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.5178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1213 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 29741 Z= 0.170 Angle : 0.718 13.978 40566 Z= 0.356 Chirality : 0.049 0.288 4694 Planarity : 0.005 0.079 5183 Dihedral : 5.164 37.865 3967 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.76 % Allowed : 15.18 % Favored : 82.05 % 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 are not related in a simple way. whole: -1.33 (0.13), residues: 3626 helix: 0.28 (0.20), residues: 646 sheet: -0.37 (0.17), residues: 863 loop : -1.52 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 100 TYR 0.025 0.002 TYR B 313 PHE 0.024 0.002 PHE A 898 TRP 0.022 0.002 TRP J 109 HIS 0.019 0.002 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (29660) covalent geometry : angle 0.70436 / 0.35 (40367) SS BOND : bond 0.00440 / 0.26 ( 44) SS BOND : angle 1.22965 / 0.82 ( 88) hydrogen bonds : bond 0.04612 / 3.04 ( 1048) hydrogen bonds : angle 6.07123 / 4.16 ( 2931) link_BETA1-4 : bond 0.00680 / 0.32 ( 5) link_BETA1-4 : angle 1.60069 / 1.01 ( 15) link_NAG-ASN : bond 0.00707 / 0.47 ( 32) link_NAG-ASN : angle 2.76678 / 2.20 ( 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 226 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 140 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.2444 (OUTLIER) cc_final: 0.1181 (m) REVERT: A 64 TRP cc_start: 0.4407 (t60) cc_final: 0.4167 (t60) REVERT: A 220 PHE cc_start: 0.0295 (t80) cc_final: -0.0503 (p90) REVERT: A 400 PHE cc_start: 0.2325 (OUTLIER) cc_final: 0.1545 (p90) REVERT: A 451 TYR cc_start: 0.1227 (m-80) cc_final: 0.0538 (m-80) REVERT: A 655 HIS cc_start: 0.3393 (OUTLIER) cc_final: -0.0160 (t-170) REVERT: A 762 GLN cc_start: 0.3139 (mm-40) cc_final: 0.2184 (tp40) REVERT: A 779 GLN cc_start: 0.0402 (OUTLIER) cc_final: -0.0963 (mt0) REVERT: A 1029 MET cc_start: -0.1298 (ttt) cc_final: -0.2026 (mtp) REVERT: A 1091 ARG cc_start: 0.3650 (mtp85) cc_final: 0.2512 (mpt-90) REVERT: B 714 ILE cc_start: -0.1663 (OUTLIER) cc_final: -0.2330 (mt) REVERT: B 797 PHE cc_start: 0.3569 (m-10) cc_final: 0.2813 (m-80) REVERT: B 916 LEU cc_start: 0.0835 (OUTLIER) cc_final: -0.1651 (mp) REVERT: B 1058 HIS cc_start: 0.1422 (OUTLIER) cc_final: 0.0711 (m-70) REVERT: C 300 LYS cc_start: 0.2327 (ttmt) cc_final: 0.1835 (mmtt) REVERT: C 355 ARG cc_start: -0.0220 (OUTLIER) cc_final: -0.2854 (ptt180) REVERT: C 432 CYS cc_start: 0.0765 (OUTLIER) cc_final: 0.0342 (p) REVERT: C 1089 PHE cc_start: 0.3442 (m-80) cc_final: 0.2447 (m-80) REVERT: C 1118 ASP cc_start: 0.3764 (t70) cc_final: 0.3540 (t70) REVERT: D 94 TYR cc_start: 0.5029 (m-80) cc_final: 0.4674 (m-80) REVERT: G 34 MET cc_start: 0.1667 (tpp) cc_final: 0.1214 (tpp) REVERT: J 109 TRP cc_start: 0.0416 (p90) cc_final: -0.0628 (p90) REVERT: K 26 SER cc_start: 0.1382 (OUTLIER) cc_final: 0.0140 (t) outliers start: 86 outliers final: 47 residues processed: 209 average time/residue: 0.1560 time to fit residues: 54.6138 Evaluate side-chains 184 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 307 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 515 PHE 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 761 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 952 VAL 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 B residue 350 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 1007 TYR 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 131 CYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 432 CYS 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 1120 THR Chi-restraints excluded: chain C residue 1129 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 D residue 106 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 169 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 342 optimal weight: 50.0000 chunk 110 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 chunk 233 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 907 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.299893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.5257 r_free = 0.5257 target = 0.291302 restraints weight = 65753.547| |-----------------------------------------------------------------------------| r_work (start): 0.5251 rms_B_bonded: 1.42 r_work: 0.5146 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.5146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1119 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29741 Z= 0.120 Angle : 0.633 11.262 40566 Z= 0.310 Chirality : 0.047 0.802 4694 Planarity : 0.004 0.073 5183 Dihedral : 4.806 38.026 3967 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.05 % Allowed : 15.86 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3626 helix: 0.66 (0.21), residues: 635 sheet: -0.32 (0.17), residues: 886 loop : -1.46 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 102 TYR 0.020 0.001 TYR B 453 PHE 0.021 0.001 PHE C 377 TRP 0.016 0.001 TRP J 109 HIS 0.013 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (29660) covalent geometry : angle 0.61657 / 0.31 (40367) SS BOND : bond 0.00362 / 0.24 ( 44) SS BOND : angle 1.32276 / 0.81 ( 88) hydrogen bonds : bond 0.03997 / 2.63 ( 1048) hydrogen bonds : angle 5.72242 / 3.92 ( 2931) link_BETA1-4 : bond 0.00739 / 0.30 ( 5) link_BETA1-4 : angle 1.24494 / 0.82 ( 15) link_NAG-ASN : bond 0.00572 / 0.37 ( 32) link_NAG-ASN : angle 2.77088 / 2.24 ( 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 196 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 132 time to evaluate : 0.944 Fit side-chains REVERT: A 29 THR cc_start: 0.2374 (OUTLIER) cc_final: 0.1007 (m) REVERT: A 64 TRP cc_start: 0.4256 (OUTLIER) cc_final: 0.4023 (t60) REVERT: A 220 PHE cc_start: 0.0136 (t80) cc_final: -0.0550 (p90) REVERT: A 400 PHE cc_start: 0.2153 (OUTLIER) cc_final: 0.1307 (p90) REVERT: A 451 TYR cc_start: 0.1243 (m-80) cc_final: 0.0630 (m-80) REVERT: A 569 ILE cc_start: -0.1042 (OUTLIER) cc_final: -0.1645 (mm) REVERT: A 762 GLN cc_start: 0.3102 (mm-40) cc_final: 0.2134 (tp40) REVERT: A 779 GLN cc_start: 0.0070 (OUTLIER) cc_final: -0.0747 (mt0) REVERT: A 1029 MET cc_start: -0.1099 (ttt) cc_final: -0.1904 (mtp) REVERT: A 1091 ARG cc_start: 0.3585 (mtp85) cc_final: 0.2687 (mpt-90) REVERT: B 313 TYR cc_start: 0.2634 (m-80) cc_final: 0.0816 (t80) REVERT: B 714 ILE cc_start: -0.1464 (OUTLIER) cc_final: -0.2079 (mt) REVERT: B 797 PHE cc_start: 0.3310 (m-10) cc_final: 0.2646 (m-80) REVERT: B 916 LEU cc_start: 0.0774 (OUTLIER) cc_final: -0.1766 (mp) REVERT: C 300 LYS cc_start: 0.2140 (ttmt) cc_final: 0.1717 (mmtm) REVERT: C 355 ARG cc_start: -0.0392 (OUTLIER) cc_final: -0.2793 (ptt-90) REVERT: C 364 ASP cc_start: 0.2170 (t0) cc_final: 0.1128 (p0) REVERT: C 432 CYS cc_start: 0.0638 (OUTLIER) cc_final: 0.0386 (p) REVERT: C 1089 PHE cc_start: 0.3089 (m-80) cc_final: 0.1905 (m-80) REVERT: C 1118 ASP cc_start: 0.3907 (t70) cc_final: 0.3641 (t70) REVERT: D 94 TYR cc_start: 0.5141 (m-80) cc_final: 0.4802 (m-80) REVERT: G 34 MET cc_start: 0.1684 (tpp) cc_final: 0.1272 (tpp) REVERT: J 109 TRP cc_start: 0.0449 (p90) cc_final: -0.0777 (p90) REVERT: K 26 SER cc_start: 0.1448 (OUTLIER) cc_final: 0.0221 (t) outliers start: 64 outliers final: 40 residues processed: 183 average time/residue: 0.1683 time to fit residues: 51.5426 Evaluate side-chains 173 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 307 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 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 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1007 TYR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 466 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 1120 THR Chi-restraints excluded: chain C residue 1129 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 H residue 70 SER 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 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 284 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 148 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 241 optimal weight: 3.9990 chunk 248 optimal weight: 0.0010 chunk 263 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 276 optimal weight: 10.0000 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 965 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.300055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.291607 restraints weight = 65612.651| |-----------------------------------------------------------------------------| r_work (start): 0.5253 rms_B_bonded: 1.42 r_work: 0.5151 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.5151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1090 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29741 Z= 0.113 Angle : 0.603 12.823 40566 Z= 0.296 Chirality : 0.045 0.365 4694 Planarity : 0.004 0.069 5183 Dihedral : 4.572 38.269 3967 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.25 % Allowed : 16.08 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3626 helix: 0.87 (0.21), residues: 630 sheet: -0.37 (0.17), residues: 868 loop : -1.31 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 466 TYR 0.019 0.001 TYR B 453 PHE 0.019 0.001 PHE C 377 TRP 0.013 0.001 TRP J 109 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (29660) covalent geometry : angle 0.59059 / 0.29 (40367) SS BOND : bond 0.00330 / 0.21 ( 44) SS BOND : angle 1.15658 / 0.73 ( 88) hydrogen bonds : bond 0.03761 / 2.45 ( 1048) hydrogen bonds : angle 5.50635 / 3.77 ( 2931) link_BETA1-4 : bond 0.00693 / 0.27 ( 5) link_BETA1-4 : angle 1.21032 / 0.79 ( 15) link_NAG-ASN : bond 0.00626 / 0.39 ( 32) link_NAG-ASN : angle 2.33671 / 1.91 ( 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 203 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 133 time to evaluate : 0.947 Fit side-chains REVERT: A 29 THR cc_start: 0.2460 (OUTLIER) cc_final: 0.0986 (m) REVERT: A 64 TRP cc_start: 0.4231 (t60) cc_final: 0.3966 (t60) REVERT: A 220 PHE cc_start: 0.0161 (t80) cc_final: -0.0462 (p90) REVERT: A 304 LYS cc_start: 0.2118 (OUTLIER) cc_final: 0.1902 (mttt) REVERT: A 400 PHE cc_start: 0.2182 (OUTLIER) cc_final: 0.1431 (p90) REVERT: A 451 TYR cc_start: 0.0895 (m-80) cc_final: 0.0255 (m-80) REVERT: A 515 PHE cc_start: -0.1223 (OUTLIER) cc_final: -0.3466 (p90) REVERT: A 762 GLN cc_start: 0.3001 (mm-40) cc_final: 0.2002 (tp40) REVERT: A 779 GLN cc_start: 0.0043 (OUTLIER) cc_final: -0.0410 (mt0) REVERT: A 1029 MET cc_start: -0.1052 (ttt) cc_final: -0.1836 (mtp) REVERT: B 697 MET cc_start: -0.0100 (mtt) cc_final: -0.2780 (mtp) REVERT: B 714 ILE cc_start: -0.1538 (OUTLIER) cc_final: -0.2093 (mt) REVERT: B 797 PHE cc_start: 0.3255 (m-10) cc_final: 0.2714 (m-80) REVERT: C 126 VAL cc_start: 0.1953 (t) cc_final: 0.1693 (p) REVERT: C 300 LYS cc_start: 0.2485 (ttmt) cc_final: 0.1960 (mmtt) REVERT: C 314 GLN cc_start: -0.0115 (OUTLIER) cc_final: -0.0319 (mp10) REVERT: C 364 ASP cc_start: 0.1978 (t0) cc_final: 0.1058 (p0) REVERT: C 432 CYS cc_start: 0.0791 (OUTLIER) cc_final: 0.0476 (p) REVERT: C 864 LEU cc_start: 0.1372 (OUTLIER) cc_final: 0.1066 (tp) REVERT: C 1089 PHE cc_start: 0.3081 (m-80) cc_final: 0.1685 (m-80) REVERT: D 94 TYR cc_start: 0.5204 (m-80) cc_final: 0.4878 (m-80) REVERT: G 34 MET cc_start: 0.1850 (tpp) cc_final: 0.1413 (tpp) REVERT: J 109 TRP cc_start: 0.0471 (p90) cc_final: -0.0833 (p90) REVERT: K 26 SER cc_start: 0.1307 (OUTLIER) cc_final: 0.0084 (t) REVERT: K 102 THR cc_start: 0.1960 (OUTLIER) cc_final: 0.0999 (p) outliers start: 70 outliers final: 42 residues processed: 192 average time/residue: 0.1654 time to fit residues: 53.2605 Evaluate side-chains 184 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 304 LYS 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 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE 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 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1040 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 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 432 CYS 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 864 LEU 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 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 H residue 70 SER 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 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 171 optimal weight: 0.0970 chunk 223 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 343 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 244 optimal weight: 40.0000 chunk 225 optimal weight: 7.9990 chunk 365 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.299031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.297469 restraints weight = 69788.456| |-----------------------------------------------------------------------------| r_work (start): 0.5318 rms_B_bonded: 0.31 r_work: 0.5282 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.5248 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.5248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1313 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 29741 Z= 0.229 Angle : 0.860 22.513 40566 Z= 0.429 Chirality : 0.053 0.455 4694 Planarity : 0.006 0.080 5183 Dihedral : 5.751 40.188 3967 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.47 % Allowed : 16.40 % Favored : 81.12 % 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 are not related in a simple way. whole: -1.56 (0.13), residues: 3626 helix: -0.12 (0.20), residues: 625 sheet: -0.59 (0.17), residues: 847 loop : -1.53 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 765 TYR 0.035 0.002 TYR A1067 PHE 0.037 0.003 PHE B 800 TRP 0.035 0.003 TRP C 353 HIS 0.014 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (29660) covalent geometry : angle 0.84625 / 0.43 (40367) SS BOND : bond 0.00391 / 0.25 ( 44) SS BOND : angle 1.50171 / 0.97 ( 88) hydrogen bonds : bond 0.05668 / 3.79 ( 1048) hydrogen bonds : angle 6.61960 / 4.53 ( 2931) link_BETA1-4 : bond 0.00979 / 0.39 ( 5) link_BETA1-4 : angle 1.59290 / 1.03 ( 15) link_NAG-ASN : bond 0.00815 / 0.56 ( 32) link_NAG-ASN : angle 2.96543 / 2.24 ( 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 216 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 139 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: -0.0103 (t80) cc_final: -0.0363 (p90) REVERT: A 400 PHE cc_start: 0.2000 (OUTLIER) cc_final: 0.1176 (p90) REVERT: A 451 TYR cc_start: 0.1293 (m-80) cc_final: 0.0774 (m-80) REVERT: A 762 GLN cc_start: 0.3994 (mm-40) cc_final: 0.2561 (tp40) REVERT: A 779 GLN cc_start: 0.0324 (OUTLIER) cc_final: -0.0777 (mt0) REVERT: A 1091 ARG cc_start: 0.3961 (mmt90) cc_final: 0.3070 (mpt-90) REVERT: A 1109 PHE cc_start: 0.2926 (OUTLIER) cc_final: 0.2653 (t80) REVERT: B 224 GLU cc_start: 0.2239 (OUTLIER) cc_final: 0.1939 (mm-30) REVERT: B 714 ILE cc_start: -0.1189 (OUTLIER) cc_final: -0.1827 (mt) REVERT: B 800 PHE cc_start: 0.2098 (m-80) cc_final: 0.1367 (m-80) REVERT: B 894 LEU cc_start: 0.4398 (mt) cc_final: 0.4180 (mp) REVERT: B 1041 ASP cc_start: 0.5049 (OUTLIER) cc_final: 0.4293 (t0) REVERT: C 241 LEU cc_start: 0.2471 (mm) cc_final: 0.1909 (mm) REVERT: C 300 LYS cc_start: 0.2609 (ttmt) cc_final: 0.2194 (mmtt) REVERT: C 314 GLN cc_start: 0.0422 (OUTLIER) cc_final: -0.0399 (mp10) REVERT: C 784 GLN cc_start: 0.0687 (mt0) cc_final: 0.0264 (pt0) REVERT: C 864 LEU cc_start: 0.1138 (OUTLIER) cc_final: 0.0593 (tt) REVERT: C 1010 GLN cc_start: 0.4566 (pt0) cc_final: 0.4341 (pt0) REVERT: C 1089 PHE cc_start: 0.3854 (m-80) cc_final: 0.2897 (m-80) REVERT: D 94 TYR cc_start: 0.5303 (m-80) cc_final: 0.4823 (m-80) REVERT: G 34 MET cc_start: 0.2481 (tpp) cc_final: 0.1996 (tpp) REVERT: J 109 TRP cc_start: 0.1084 (p90) cc_final: 0.0709 (p90) REVERT: K 4 MET cc_start: 0.4102 (pmm) cc_final: 0.3638 (ptp) REVERT: K 102 THR cc_start: 0.1609 (OUTLIER) cc_final: 0.0889 (p) outliers start: 77 outliers final: 49 residues processed: 203 average time/residue: 0.1596 time to fit residues: 54.5609 Evaluate side-chains 189 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP 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 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE 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 1066 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1041 ASP 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 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 314 GLN 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 662 CYS Chi-restraints excluded: chain C residue 864 LEU 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 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 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 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 125 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 338 optimal weight: 0.8980 chunk 67 optimal weight: 0.0020 chunk 343 optimal weight: 40.0000 chunk 70 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 336 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 777 ASN A1058 HIS B 774 GLN B 907 ASN B 949 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 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 = 0.5335 r_free = 0.5335 target = 0.299260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5289 r_free = 0.5289 target = 0.294663 restraints weight = 68596.488| |-----------------------------------------------------------------------------| r_work (start): 0.5283 rms_B_bonded: 0.85 r_work: 0.5219 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.5173 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.5173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1276 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29741 Z= 0.130 Angle : 0.653 11.715 40566 Z= 0.323 Chirality : 0.047 0.369 4694 Planarity : 0.005 0.070 5183 Dihedral : 4.988 39.222 3967 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.73 % Allowed : 17.01 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3626 helix: 0.43 (0.21), residues: 621 sheet: -0.52 (0.17), residues: 834 loop : -1.42 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.019 0.001 TYR B 453 PHE 0.020 0.001 PHE B 800 TRP 0.014 0.001 TRP J 109 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (29660) covalent geometry : angle 0.63865 / 0.32 (40367) SS BOND : bond 0.00743 / 0.52 ( 44) SS BOND : angle 1.60691 / 1.04 ( 88) hydrogen bonds : bond 0.04213 / 2.78 ( 1048) hydrogen bonds : angle 5.90899 / 4.03 ( 2931) link_BETA1-4 : bond 0.00800 / 0.32 ( 5) link_BETA1-4 : angle 1.32456 / 0.87 ( 15) link_NAG-ASN : bond 0.00591 / 0.38 ( 32) link_NAG-ASN : angle 2.48265 / 1.96 ( 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 183 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.5004 (t60) cc_final: 0.4149 (t60) REVERT: A 278 LYS cc_start: 0.2146 (tmtt) cc_final: 0.1732 (mmtt) REVERT: A 400 PHE cc_start: 0.2259 (OUTLIER) cc_final: 0.1511 (p90) REVERT: A 451 TYR cc_start: 0.0887 (m-80) cc_final: 0.0080 (m-80) REVERT: A 581 THR cc_start: 0.1911 (OUTLIER) cc_final: 0.1646 (m) REVERT: A 732 THR cc_start: 0.5029 (OUTLIER) cc_final: 0.4785 (p) REVERT: A 762 GLN cc_start: 0.4025 (mm-40) cc_final: 0.2570 (tp40) REVERT: A 779 GLN cc_start: 0.0190 (OUTLIER) cc_final: -0.1160 (mt0) REVERT: B 386 LYS cc_start: 0.0027 (ptpt) cc_final: -0.0395 (mtmm) REVERT: B 697 MET cc_start: 0.0243 (mtt) cc_final: -0.2233 (mtm) REVERT: B 714 ILE cc_start: -0.1436 (OUTLIER) cc_final: -0.2066 (mt) REVERT: B 797 PHE cc_start: 0.3388 (m-10) cc_final: 0.2895 (m-80) REVERT: B 800 PHE cc_start: 0.1863 (m-80) cc_final: 0.1167 (m-80) REVERT: C 241 LEU cc_start: 0.2992 (mm) cc_final: 0.2344 (mm) REVERT: C 364 ASP cc_start: 0.2049 (t0) cc_final: 0.1142 (p0) REVERT: C 784 GLN cc_start: 0.0553 (mt0) cc_final: 0.0218 (pt0) REVERT: C 864 LEU cc_start: 0.1583 (OUTLIER) cc_final: 0.1306 (tp) REVERT: C 988 GLU cc_start: 0.0114 (OUTLIER) cc_final: -0.0379 (mm-30) REVERT: D 94 TYR cc_start: 0.5534 (m-80) cc_final: 0.5008 (m-80) REVERT: G 34 MET cc_start: 0.2106 (tpp) cc_final: 0.1696 (tpp) REVERT: J 109 TRP cc_start: 0.0550 (p90) cc_final: 0.0194 (p90) REVERT: K 4 MET cc_start: 0.4033 (pmm) cc_final: 0.3670 (ptp) REVERT: K 95 GLN cc_start: 0.2667 (pp30) cc_final: 0.1687 (pm20) outliers start: 54 outliers final: 45 residues processed: 173 average time/residue: 0.1730 time to fit residues: 49.9350 Evaluate side-chains 175 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 614 ASP Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE 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 1066 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 599 THR 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 1040 VAL 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 207 HIS 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 864 LEU 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 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 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 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 189 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 186 optimal weight: 0.0170 chunk 353 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 356 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 314 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.299331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.294682 restraints weight = 69291.033| |-----------------------------------------------------------------------------| r_work (start): 0.5290 rms_B_bonded: 0.87 r_work: 0.5219 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.5173 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.5173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1280 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29741 Z= 0.125 Angle : 0.634 11.635 40566 Z= 0.313 Chirality : 0.046 0.350 4694 Planarity : 0.005 0.069 5183 Dihedral : 4.765 38.869 3967 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.93 % Allowed : 16.85 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3626 helix: 0.58 (0.21), residues: 628 sheet: -0.51 (0.17), residues: 861 loop : -1.37 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1039 TYR 0.019 0.001 TYR A1067 PHE 0.021 0.001 PHE C 377 TRP 0.016 0.001 TRP D 36 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (29660) covalent geometry : angle 0.62016 / 0.31 (40367) SS BOND : bond 0.00363 / 0.24 ( 44) SS BOND : angle 1.39779 / 0.91 ( 88) hydrogen bonds : bond 0.03985 / 2.62 ( 1048) hydrogen bonds : angle 5.71450 / 3.91 ( 2931) link_BETA1-4 : bond 0.00580 / 0.27 ( 5) link_BETA1-4 : angle 1.40839 / 0.92 ( 15) link_NAG-ASN : bond 0.00542 / 0.36 ( 32) link_NAG-ASN : angle 2.40151 / 1.94 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5943.12 seconds wall clock time: 103 minutes 4.37 seconds (6184.37 seconds total)