Starting phenix.real_space_refine on Wed Jun 25 03:18:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7chh_30374/06_2025/7chh_30374.cif Found real_map, /net/cci-nas-00/data/ceres_data/7chh_30374/06_2025/7chh_30374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7chh_30374/06_2025/7chh_30374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7chh_30374/06_2025/7chh_30374.map" model { file = "/net/cci-nas-00/data/ceres_data/7chh_30374/06_2025/7chh_30374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7chh_30374/06_2025/7chh_30374.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 1.50s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG: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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "G" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "H" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "J" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 18.23, per 1000 atoms: 0.63 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: 6.93 Conformation dependent library (CDL) restraints added in 4.0 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: 4.64 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: 16.45 Time building geometry restraints manager: 8.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 9318 1.35 - 1.48: 8012 1.48 - 1.62: 12165 1.62 - 1.75: 2 1.75 - 1.89: 163 Bond restraints: 29660 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.86e+00 bond pdb=" CA TRP J 109 " pdb=" C TRP J 109 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.72e-02 3.38e+03 8.16e+00 bond pdb=" CB ARG D 43 " pdb=" CG ARG D 43 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.87e+00 bond pdb=" CB ARG J 43 " pdb=" CG ARG J 43 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.81e+00 ... (remaining 29655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 39507 3.13 - 6.26: 710 6.26 - 9.39: 107 9.39 - 12.51: 32 12.51 - 15.64: 11 Bond angle restraints: 40367 Sorted by residual: angle pdb=" CB ARG G 100 " pdb=" CG ARG G 100 " pdb=" CD ARG G 100 " ideal model delta sigma weight residual 111.30 95.66 15.64 2.30e+00 1.89e-01 4.63e+01 angle pdb=" CB ARG J 100 " pdb=" CG ARG J 100 " pdb=" CD ARG J 100 " ideal model delta sigma weight residual 111.30 95.67 15.63 2.30e+00 1.89e-01 4.62e+01 angle pdb=" CB ARG D 100 " pdb=" CG ARG D 100 " pdb=" CD ARG D 100 " ideal model delta sigma weight residual 111.30 95.72 15.58 2.30e+00 1.89e-01 4.59e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 128.88 -14.48 2.30e+00 1.89e-01 3.96e+01 angle pdb=" C ASN A 165 " pdb=" N CYS A 166 " pdb=" CA CYS A 166 " ideal model delta sigma weight residual 122.74 111.32 11.42 1.82e+00 3.02e-01 3.94e+01 ... (remaining 40362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 16673 21.99 - 43.98: 1213 43.98 - 65.98: 213 65.98 - 87.97: 39 87.97 - 109.96: 5 Dihedral angle restraints: 18143 sinusoidal: 7454 harmonic: 10689 Sorted by residual: dihedral pdb=" CA LEU B 293 " pdb=" C LEU B 293 " pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta harmonic sigma weight residual -180.00 -117.24 -62.76 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.81 -85.19 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 177.64 -84.64 1 1.00e+01 1.00e-02 8.70e+01 ... (remaining 18140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3924 0.082 - 0.164: 689 0.164 - 0.246: 61 0.246 - 0.327: 10 0.327 - 0.409: 10 Chirality restraints: 4694 Sorted by residual: chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CB ILE C 666 " pdb=" CA ILE C 666 " pdb=" CG1 ILE C 666 " pdb=" CG2 ILE C 666 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C2 NAG C1308 " pdb=" C1 NAG C1308 " pdb=" C3 NAG C1308 " pdb=" N2 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 4691 not shown) Planarity restraints: 5215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 29 " 0.025 2.00e-02 2.50e+03 3.54e-02 2.19e+01 pdb=" CG PHE J 29 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE J 29 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE J 29 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE J 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE J 29 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE J 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 29 " -0.025 2.00e-02 2.50e+03 3.53e-02 2.18e+01 pdb=" CG PHE D 29 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE D 29 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE D 29 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE D 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 29 " -0.025 2.00e-02 2.50e+03 3.51e-02 2.16e+01 pdb=" CG PHE G 29 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE G 29 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE G 29 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE G 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 29 " -0.000 2.00e-02 2.50e+03 ... (remaining 5212 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1627 2.73 - 3.27: 26607 3.27 - 3.81: 47275 3.81 - 4.36: 54094 4.36 - 4.90: 95682 Nonbonded interactions: 225285 Sorted by model distance: nonbonded pdb=" O GLY D 116 " pdb=" OG SER E 48 " model vdw 2.182 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 2.253 3.120 nonbonded pdb=" O SER D 85 " pdb=" OG SER D 85 " model vdw 2.257 3.040 nonbonded pdb=" O SER G 85 " pdb=" OG SER G 85 " model vdw 2.257 3.040 nonbonded pdb=" O SER J 85 " pdb=" OG SER J 85 " model vdw 2.257 3.040 ... (remaining 225280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 95 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA or n \ ame C or name O or name CB )) or resid 130 through 140 or (resid 157 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or resid 217 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 243 or resid 264 through 516 or resid 521 through 620 or resid 641 t \ hrough 1146 or resid 1301 through 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 1146 or resid 1301 through 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 1146 or resid 1301 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.140 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 71.900 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0174 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 29741 Z= 0.319 Angle : 1.125 15.643 40566 Z= 0.594 Chirality : 0.063 0.409 4694 Planarity : 0.007 0.085 5183 Dihedral : 15.259 109.961 11157 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.004 TRP C 353 HIS 0.013 0.002 HIS A1058 PHE 0.080 0.004 PHE J 29 TYR 0.038 0.003 TYR C 423 ARG 0.056 0.002 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 32) link_NAG-ASN : angle 3.82195 ( 96) link_BETA1-4 : bond 0.01057 ( 5) link_BETA1-4 : angle 2.91849 ( 15) hydrogen bonds : bond 0.22590 ( 1048) hydrogen bonds : angle 9.29396 ( 2931) SS BOND : bond 0.01091 ( 44) SS BOND : angle 2.83893 ( 88) covalent geometry : bond 0.00726 (29660) covalent geometry : angle 1.10335 (40367) *********************** 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 : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1151 (m-80) cc_final: 0.0764 (m-80) REVERT: A 618 THR cc_start: 0.0081 (m) cc_final: -0.0948 (p) REVERT: A 823 PHE cc_start: 0.0703 (m-10) cc_final: -0.2134 (p90) REVERT: A 1029 MET cc_start: 0.0721 (tpp) cc_final: -0.0305 (tpp) REVERT: A 1110 TYR cc_start: 0.0702 (t80) cc_final: -0.0282 (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: 0.0880 (tpt170) REVERT: B 1115 ILE cc_start: 0.2112 (mt) cc_final: 0.1515 (pt) REVERT: E 94 MET cc_start: -0.4673 (ttp) cc_final: -0.4906 (ttp) REVERT: G 4 LEU cc_start: -0.0684 (OUTLIER) cc_final: -0.1367 (mm) REVERT: G 34 MET cc_start: 0.0140 (OUTLIER) cc_final: -0.0383 (tpp) REVERT: G 52 SER cc_start: 0.1959 (OUTLIER) cc_final: 0.1480 (m) REVERT: G 53 ASP cc_start: 0.0272 (OUTLIER) cc_final: -0.0623 (m-30) REVERT: H 41 TYR cc_start: -0.0516 (OUTLIER) cc_final: -0.1296 (m-80) REVERT: H 76 PHE cc_start: 0.0814 (OUTLIER) cc_final: -0.0258 (m-10) REVERT: H 111 ILE cc_start: -0.0088 (OUTLIER) cc_final: -0.0451 (tt) REVERT: J 52 SER cc_start: -0.0323 (OUTLIER) cc_final: -0.0807 (p) REVERT: J 105 TYR cc_start: -0.3500 (m-80) cc_final: -0.3790 (m-80) REVERT: K 11 LEU cc_start: -0.2711 (OUTLIER) cc_final: -0.2953 (tp) REVERT: K 41 TYR cc_start: 0.0873 (OUTLIER) cc_final: 0.0240 (m-80) REVERT: K 51 LEU cc_start: 0.0056 (OUTLIER) cc_final: -0.0369 (tt) outliers start: 111 outliers final: 28 residues processed: 338 average time/residue: 0.4347 time to fit residues: 236.3011 Evaluate side-chains 174 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 2.734 ------------------------------------------------------------------------------- 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 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 51 LEU 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 309 optimal weight: 1.9990 chunk 278 optimal weight: 40.0000 chunk 154 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 187 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 287 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 174 optimal weight: 0.2980 chunk 214 optimal weight: 1.9990 chunk 333 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 965 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 563 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1048 HIS C 901 GLN C 954 GLN C1010 GLN C1106 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5354 r_free = 0.5354 target = 0.302509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.295259 restraints weight = 66850.714| |-----------------------------------------------------------------------------| r_work (start): 0.5282 rms_B_bonded: 1.30 r_work: 0.5190 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.5190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0495 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 29741 Z= 0.156 Angle : 0.711 12.964 40566 Z= 0.358 Chirality : 0.048 0.554 4694 Planarity : 0.005 0.090 5183 Dihedral : 8.446 104.752 4902 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 1.48 % Allowed : 7.58 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3626 helix: 0.25 (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 TRP 0.022 0.002 TRP J 47 HIS 0.008 0.001 HIS A 655 PHE 0.023 0.002 PHE B 238 TYR 0.025 0.002 TYR B 204 ARG 0.010 0.001 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 32) link_NAG-ASN : angle 3.18789 ( 96) link_BETA1-4 : bond 0.00608 ( 5) link_BETA1-4 : angle 1.86209 ( 15) hydrogen bonds : bond 0.04791 ( 1048) hydrogen bonds : angle 6.42593 ( 2931) SS BOND : bond 0.00473 ( 44) SS BOND : angle 1.71601 ( 88) covalent geometry : bond 0.00333 (29660) covalent geometry : angle 0.69037 (40367) *********************** 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 202 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1038 (m-80) cc_final: 0.0718 (m-80) REVERT: A 618 THR cc_start: 0.1000 (m) cc_final: -0.0455 (p) REVERT: A 1110 TYR cc_start: 0.1528 (t80) cc_final: 0.0169 (t80) REVERT: B 614 ASP cc_start: -0.0026 (p0) cc_final: -0.0323 (t0) REVERT: B 1014 ARG cc_start: 0.2613 (ttm110) cc_final: 0.0697 (tpp-160) REVERT: C 355 ARG cc_start: 0.0060 (OUTLIER) cc_final: -0.2663 (ptt180) REVERT: C 1089 PHE cc_start: 0.3393 (m-80) cc_final: 0.2794 (m-80) REVERT: C 1111 GLU cc_start: 0.0350 (tt0) cc_final: -0.0255 (mm-30) REVERT: E 94 MET cc_start: -0.2634 (ttp) cc_final: -0.2978 (ttp) REVERT: G 4 LEU cc_start: 0.0590 (OUTLIER) cc_final: 0.0159 (mt) REVERT: H 54 TYR cc_start: 0.1227 (OUTLIER) cc_final: 0.0362 (p90) REVERT: J 105 TYR cc_start: -0.2132 (m-80) cc_final: -0.2932 (m-80) REVERT: K 26 SER cc_start: 0.0635 (OUTLIER) cc_final: -0.0648 (t) outliers start: 46 outliers final: 19 residues processed: 190 average time/residue: 0.4265 time to fit residues: 130.8331 Evaluate side-chains 153 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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 51 ILE 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 G residue 4 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain J residue 51 ILE 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 55 LEU Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 94 MET 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 178 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 208 optimal weight: 40.0000 chunk 335 optimal weight: 40.0000 chunk 230 optimal weight: 5.9990 chunk 193 optimal weight: 0.1980 chunk 170 optimal weight: 0.7980 chunk 203 optimal weight: 0.2980 chunk 244 optimal weight: 30.0000 chunk 328 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 388 ASN B 409 GLN B 501 ASN B 901 GLN B 913 GLN B 949 GLN B 957 GLN B1058 HIS B1101 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 343 ASN C 957 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.299955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.295803 restraints weight = 69675.486| |-----------------------------------------------------------------------------| r_work (start): 0.5290 rms_B_bonded: 0.79 r_work: 0.5225 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.5183 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.5183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1130 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.293 29741 Z= 0.256 Angle : 0.920 18.520 40566 Z= 0.461 Chirality : 0.054 0.359 4694 Planarity : 0.007 0.121 5183 Dihedral : 8.635 97.744 4835 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 2.83 % Allowed : 11.36 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3626 helix: -0.58 (0.19), residues: 663 sheet: -0.48 (0.17), residues: 902 loop : -1.56 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 109 HIS 0.013 0.002 HIS A 49 PHE 0.042 0.003 PHE B 927 TYR 0.032 0.003 TYR A1067 ARG 0.013 0.001 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00841 ( 32) link_NAG-ASN : angle 3.15038 ( 96) link_BETA1-4 : bond 0.01277 ( 5) link_BETA1-4 : angle 2.47606 ( 15) hydrogen bonds : bond 0.06081 ( 1048) hydrogen bonds : angle 6.88060 ( 2931) SS BOND : bond 0.01900 ( 44) SS BOND : angle 1.47033 ( 88) covalent geometry : bond 0.00576 (29660) covalent geometry : angle 0.90543 (40367) *********************** 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 229 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 141 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2381 (OUTLIER) cc_final: 0.1467 (m) REVERT: A 451 TYR cc_start: 0.1482 (m-80) cc_final: 0.1039 (m-80) REVERT: A 536 ASN cc_start: -0.0106 (OUTLIER) cc_final: -0.0523 (m-40) REVERT: A 714 ILE cc_start: -0.1412 (OUTLIER) cc_final: -0.2040 (pt) REVERT: A 762 GLN cc_start: 0.2261 (mm110) cc_final: 0.1576 (tp40) REVERT: A 779 GLN cc_start: 0.0275 (OUTLIER) cc_final: -0.1083 (mt0) REVERT: A 990 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.5160 (tt0) REVERT: A 1110 TYR cc_start: 0.3540 (t80) cc_final: 0.1556 (t80) REVERT: A 1130 ILE cc_start: 0.0815 (OUTLIER) cc_final: 0.0426 (mt) REVERT: A 1135 ASN cc_start: -0.0988 (OUTLIER) cc_final: -0.2065 (t0) REVERT: B 53 ASP cc_start: 0.0945 (OUTLIER) cc_final: 0.0365 (t70) REVERT: B 206 LYS cc_start: 0.2337 (tttt) cc_final: 0.2077 (tttt) REVERT: B 714 ILE cc_start: -0.1535 (OUTLIER) cc_final: -0.2285 (mt) REVERT: B 1058 HIS cc_start: 0.1613 (OUTLIER) cc_final: 0.1024 (m-70) REVERT: C 300 LYS cc_start: 0.2341 (ttmt) cc_final: 0.1834 (mmtt) REVERT: C 355 ARG cc_start: -0.0113 (OUTLIER) cc_final: -0.2926 (ptt180) REVERT: C 432 CYS cc_start: 0.1191 (OUTLIER) cc_final: 0.0734 (p) REVERT: C 484 GLU cc_start: 0.2623 (pt0) cc_final: 0.2319 (mp0) REVERT: C 1089 PHE cc_start: 0.4067 (m-80) cc_final: 0.3270 (m-80) REVERT: C 1106 GLN cc_start: 0.1311 (OUTLIER) cc_final: -0.0778 (mm-40) REVERT: C 1111 GLU cc_start: 0.0798 (tt0) cc_final: -0.0004 (mm-30) REVERT: D 36 TRP cc_start: 0.0628 (m100) cc_final: 0.0392 (m100) REVERT: D 80 TYR cc_start: 0.2818 (m-80) cc_final: 0.2585 (m-80) REVERT: E 94 MET cc_start: -0.2541 (ttp) cc_final: -0.2845 (ttp) REVERT: K 26 SER cc_start: 0.0721 (OUTLIER) cc_final: -0.0736 (t) outliers start: 88 outliers final: 31 residues processed: 215 average time/residue: 0.4343 time to fit residues: 153.9014 Evaluate side-chains 167 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 536 ASN 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 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain K residue 26 SER 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 61 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 282 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 267 optimal weight: 0.1980 chunk 110 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 804 GLN B1064 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1036 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.299230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.290883 restraints weight = 66317.051| |-----------------------------------------------------------------------------| r_work (start): 0.5255 rms_B_bonded: 1.47 r_work: 0.5158 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.5158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1028 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29741 Z= 0.134 Angle : 0.661 10.912 40566 Z= 0.328 Chirality : 0.046 0.269 4694 Planarity : 0.005 0.088 5183 Dihedral : 7.372 95.996 4828 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 1.64 % Allowed : 14.09 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3626 helix: 0.22 (0.20), residues: 642 sheet: -0.43 (0.17), residues: 889 loop : -1.51 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 109 HIS 0.010 0.001 HIS B1058 PHE 0.023 0.001 PHE C 377 TYR 0.030 0.001 TYR B 204 ARG 0.024 0.001 ARG J 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 32) link_NAG-ASN : angle 2.85890 ( 96) link_BETA1-4 : bond 0.00783 ( 5) link_BETA1-4 : angle 2.02434 ( 15) hydrogen bonds : bond 0.04376 ( 1048) hydrogen bonds : angle 6.17334 ( 2931) SS BOND : bond 0.00527 ( 44) SS BOND : angle 1.47285 ( 88) covalent geometry : bond 0.00291 (29660) covalent geometry : angle 0.64336 (40367) *********************** 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 177 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.1286 (m-80) cc_final: 0.0649 (m-80) REVERT: A 762 GLN cc_start: 0.2504 (mm110) cc_final: 0.1486 (tp40) REVERT: A 898 PHE cc_start: 0.0606 (t80) cc_final: 0.0309 (t80) REVERT: B 797 PHE cc_start: 0.3335 (m-10) cc_final: 0.2043 (m-80) REVERT: C 300 LYS cc_start: 0.2360 (ttmt) cc_final: 0.1805 (mmtt) REVERT: C 355 ARG cc_start: -0.0280 (OUTLIER) cc_final: -0.2876 (ptt180) REVERT: C 417 LYS cc_start: 0.1965 (tppt) cc_final: 0.1658 (mmmm) REVERT: C 432 CYS cc_start: 0.0890 (OUTLIER) cc_final: 0.0437 (p) REVERT: C 1089 PHE cc_start: 0.3300 (m-80) cc_final: 0.2233 (m-80) REVERT: C 1106 GLN cc_start: 0.1440 (OUTLIER) cc_final: -0.0048 (mp10) REVERT: C 1111 GLU cc_start: 0.0595 (tt0) cc_final: 0.0012 (mm-30) REVERT: D 36 TRP cc_start: 0.0695 (m100) cc_final: 0.0431 (m100) REVERT: D 80 TYR cc_start: 0.2989 (m-80) cc_final: 0.2748 (m-80) REVERT: J 35 ASN cc_start: -0.2579 (OUTLIER) cc_final: -0.3530 (t0) REVERT: K 26 SER cc_start: 0.0804 (OUTLIER) cc_final: -0.0433 (t) outliers start: 51 outliers final: 26 residues processed: 168 average time/residue: 0.4062 time to fit residues: 113.3975 Evaluate side-chains 152 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 67 optimal weight: 0.0570 chunk 146 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 161 optimal weight: 0.1980 chunk 296 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 281 optimal weight: 9.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1058 HIS B1106 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5342 r_free = 0.5342 target = 0.300313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.298839 restraints weight = 69950.245| |-----------------------------------------------------------------------------| r_work (start): 0.5320 rms_B_bonded: 0.29 r_work: 0.5286 rms_B_bonded: 0.60 restraints_weight: 0.5000 r_work: 0.5264 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work: 0.5209 rms_B_bonded: 3.89 restraints_weight: 0.1250 r_work (final): 0.5209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1218 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 29741 Z= 0.190 Angle : 0.776 17.560 40566 Z= 0.385 Chirality : 0.050 0.329 4694 Planarity : 0.006 0.087 5183 Dihedral : 7.562 87.710 4828 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 3.37 % Allowed : 15.60 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3626 helix: 0.10 (0.20), residues: 626 sheet: -0.51 (0.17), residues: 918 loop : -1.68 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 109 HIS 0.014 0.002 HIS A 49 PHE 0.028 0.002 PHE B 927 TYR 0.032 0.002 TYR A1067 ARG 0.009 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00750 ( 32) link_NAG-ASN : angle 3.02530 ( 96) link_BETA1-4 : bond 0.00812 ( 5) link_BETA1-4 : angle 2.52928 ( 15) hydrogen bonds : bond 0.05085 ( 1048) hydrogen bonds : angle 6.41354 ( 2931) SS BOND : bond 0.01248 ( 44) SS BOND : angle 1.58994 ( 88) covalent geometry : bond 0.00427 (29660) covalent geometry : angle 0.75891 (40367) *********************** 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 243 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 138 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.0139 (t80) cc_final: -0.0682 (p90) REVERT: A 451 TYR cc_start: 0.1320 (m-80) cc_final: 0.0773 (m-80) REVERT: A 619 GLU cc_start: 0.3636 (OUTLIER) cc_final: 0.3131 (tt0) REVERT: A 779 GLN cc_start: 0.0433 (OUTLIER) cc_final: -0.0653 (mt0) REVERT: A 898 PHE cc_start: 0.1924 (t80) cc_final: 0.1437 (t80) REVERT: A 1091 ARG cc_start: 0.3151 (mtp85) cc_final: 0.1837 (mpt-90) REVERT: A 1127 ASP cc_start: 0.2610 (OUTLIER) cc_final: 0.1937 (m-30) REVERT: A 1130 ILE cc_start: 0.1107 (OUTLIER) cc_final: 0.0681 (mt) REVERT: B 189 LEU cc_start: 0.3135 (OUTLIER) cc_final: 0.2659 (mp) REVERT: B 714 ILE cc_start: -0.1525 (OUTLIER) cc_final: -0.2388 (mt) REVERT: B 797 PHE cc_start: 0.3797 (m-10) cc_final: 0.2782 (m-80) REVERT: B 909 ILE cc_start: -0.0350 (OUTLIER) cc_final: -0.1471 (pt) REVERT: B 1058 HIS cc_start: 0.1689 (OUTLIER) cc_final: 0.1269 (m-70) REVERT: B 1072 GLU cc_start: 0.2350 (OUTLIER) cc_final: 0.1158 (pm20) REVERT: B 1092 GLU cc_start: 0.2084 (OUTLIER) cc_final: 0.1558 (pt0) REVERT: C 300 LYS cc_start: 0.2744 (ttmt) cc_final: 0.2046 (mmtt) REVERT: C 314 GLN cc_start: -0.0294 (OUTLIER) cc_final: -0.0624 (mp10) REVERT: C 355 ARG cc_start: 0.0858 (OUTLIER) cc_final: -0.2206 (ptt180) REVERT: C 432 CYS cc_start: 0.1257 (OUTLIER) cc_final: 0.0884 (p) REVERT: C 780 GLU cc_start: 0.2892 (OUTLIER) cc_final: 0.2199 (tt0) REVERT: C 988 GLU cc_start: 0.0900 (OUTLIER) cc_final: 0.0303 (mm-30) REVERT: C 1089 PHE cc_start: 0.3717 (m-80) cc_final: 0.2620 (m-80) REVERT: C 1106 GLN cc_start: 0.1533 (OUTLIER) cc_final: -0.0495 (mp10) REVERT: C 1111 GLU cc_start: 0.0677 (tt0) cc_final: 0.0238 (mm-30) REVERT: G 34 MET cc_start: 0.2264 (tpp) cc_final: 0.1565 (tpp) REVERT: J 109 TRP cc_start: 0.0397 (p90) cc_final: -0.1067 (p90) REVERT: K 26 SER cc_start: 0.0628 (OUTLIER) cc_final: -0.0703 (t) outliers start: 105 outliers final: 53 residues processed: 232 average time/residue: 0.5177 time to fit residues: 199.0128 Evaluate side-chains 197 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 127 time to evaluate : 3.358 ------------------------------------------------------------------------------- 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 317 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 619 GLU 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 1004 LEU Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 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 886 TRP Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL 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 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 780 GLU 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 1086 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 145 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 224 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 607 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1058 HIS B 907 ASN C 613 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.298754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5253 r_free = 0.5253 target = 0.290630 restraints weight = 65410.873| |-----------------------------------------------------------------------------| r_work (start): 0.5253 rms_B_bonded: 1.51 r_work: 0.5152 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.5152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1191 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29741 Z= 0.126 Angle : 0.638 10.910 40566 Z= 0.315 Chirality : 0.046 0.284 4694 Planarity : 0.005 0.079 5183 Dihedral : 6.812 82.629 4828 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 2.38 % Allowed : 17.14 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3626 helix: 0.50 (0.21), residues: 627 sheet: -0.52 (0.17), residues: 921 loop : -1.52 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.015 0.001 HIS B1058 PHE 0.028 0.001 PHE C 377 TYR 0.017 0.001 TYR B 204 ARG 0.005 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 32) link_NAG-ASN : angle 2.76634 ( 96) link_BETA1-4 : bond 0.00659 ( 5) link_BETA1-4 : angle 2.35266 ( 15) hydrogen bonds : bond 0.04202 ( 1048) hydrogen bonds : angle 5.97392 ( 2931) SS BOND : bond 0.00349 ( 44) SS BOND : angle 1.30177 ( 88) covalent geometry : bond 0.00275 (29660) covalent geometry : angle 0.62008 (40367) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 136 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.0380 (t80) cc_final: -0.0482 (p90) REVERT: A 451 TYR cc_start: 0.0645 (m-80) cc_final: -0.0002 (m-80) REVERT: A 569 ILE cc_start: -0.0834 (OUTLIER) cc_final: -0.1386 (mm) REVERT: A 762 GLN cc_start: 0.3238 (mm-40) cc_final: 0.2157 (tp40) REVERT: A 898 PHE cc_start: 0.1913 (t80) cc_final: 0.1601 (t80) REVERT: A 1029 MET cc_start: -0.0941 (ttt) cc_final: -0.1985 (mtp) REVERT: A 1091 ARG cc_start: 0.3151 (mtp85) cc_final: 0.2076 (ptm160) REVERT: B 228 ASP cc_start: 0.1359 (OUTLIER) cc_final: 0.0692 (m-30) REVERT: B 313 TYR cc_start: 0.2743 (m-80) cc_final: 0.0820 (t80) REVERT: B 731 MET cc_start: -0.1285 (OUTLIER) cc_final: -0.1513 (pmm) REVERT: B 905 ARG cc_start: -0.0295 (OUTLIER) cc_final: -0.1275 (mtt-85) REVERT: B 1116 THR cc_start: -0.0704 (OUTLIER) cc_final: -0.2736 (t) REVERT: C 364 ASP cc_start: 0.2039 (t0) cc_final: 0.1038 (p0) REVERT: C 432 CYS cc_start: 0.0849 (OUTLIER) cc_final: 0.0517 (p) REVERT: C 1089 PHE cc_start: 0.3196 (m-80) cc_final: 0.1870 (m-80) REVERT: C 1106 GLN cc_start: 0.1525 (OUTLIER) cc_final: -0.0343 (mp10) REVERT: C 1111 GLU cc_start: 0.0539 (tt0) cc_final: 0.0169 (mm-30) REVERT: G 34 MET cc_start: 0.1756 (tpp) cc_final: 0.1085 (tpp) REVERT: J 35 ASN cc_start: -0.2529 (OUTLIER) cc_final: -0.3077 (t0) REVERT: J 109 TRP cc_start: 0.0032 (p90) cc_final: -0.0385 (p90) REVERT: K 97 LEU cc_start: -0.0119 (mt) cc_final: -0.0664 (mt) outliers start: 74 outliers final: 45 residues processed: 200 average time/residue: 0.3894 time to fit residues: 128.9217 Evaluate side-chains 180 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 468 ILE 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 866 THR 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 1004 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1116 THR 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 432 CYS Chi-restraints excluded: chain C residue 613 GLN 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 1081 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 356 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 61 optimal weight: 0.0050 chunk 1 optimal weight: 0.8980 chunk 278 optimal weight: 0.2980 chunk 146 optimal weight: 5.9990 chunk 57 optimal weight: 0.0000 chunk 119 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** 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 = 0.299699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.5259 r_free = 0.5259 target = 0.291277 restraints weight = 65291.583| |-----------------------------------------------------------------------------| r_work (start): 0.5253 rms_B_bonded: 1.40 r_work: 0.5150 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.5150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1121 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29741 Z= 0.107 Angle : 0.598 11.251 40566 Z= 0.294 Chirality : 0.045 0.281 4694 Planarity : 0.004 0.073 5183 Dihedral : 6.298 74.593 4828 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.62 % Rotamer: Outliers : 2.25 % Allowed : 17.46 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3626 helix: 0.83 (0.21), residues: 622 sheet: -0.42 (0.17), residues: 932 loop : -1.41 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 36 HIS 0.003 0.001 HIS C1088 PHE 0.026 0.001 PHE C 377 TYR 0.017 0.001 TYR B 204 ARG 0.005 0.000 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 32) link_NAG-ASN : angle 2.62843 ( 96) link_BETA1-4 : bond 0.00469 ( 5) link_BETA1-4 : angle 2.49035 ( 15) hydrogen bonds : bond 0.03810 ( 1048) hydrogen bonds : angle 5.65396 ( 2931) SS BOND : bond 0.00322 ( 44) SS BOND : angle 1.15712 ( 88) covalent geometry : bond 0.00232 (29660) covalent geometry : angle 0.58067 (40367) *********************** 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 201 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 131 time to evaluate : 2.684 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.2124 (OUTLIER) cc_final: 0.1002 (m) REVERT: A 220 PHE cc_start: 0.0214 (t80) cc_final: -0.0514 (p90) REVERT: A 451 TYR cc_start: 0.0486 (m-80) cc_final: -0.0171 (m-80) REVERT: A 762 GLN cc_start: 0.3138 (mm-40) cc_final: 0.2087 (tp40) REVERT: A 877 LEU cc_start: 0.3587 (OUTLIER) cc_final: 0.2026 (tp) REVERT: A 898 PHE cc_start: 0.2014 (t80) cc_final: 0.1774 (t80) REVERT: A 1029 MET cc_start: -0.1006 (ttt) cc_final: -0.1909 (mtp) REVERT: A 1091 ARG cc_start: 0.3358 (mtp85) cc_final: 0.2361 (ptp-170) REVERT: B 313 TYR cc_start: 0.2645 (m-80) cc_final: 0.0796 (t80) REVERT: B 714 ILE cc_start: -0.1564 (OUTLIER) cc_final: -0.2334 (mt) REVERT: B 731 MET cc_start: -0.1191 (OUTLIER) cc_final: -0.1464 (pmm) REVERT: C 64 TRP cc_start: 0.2066 (t60) cc_final: 0.1281 (t60) REVERT: C 364 ASP cc_start: 0.2090 (t0) cc_final: 0.1133 (p0) REVERT: C 432 CYS cc_start: 0.0783 (OUTLIER) cc_final: 0.0438 (p) REVERT: C 988 GLU cc_start: 0.0265 (OUTLIER) cc_final: -0.0487 (tp30) REVERT: C 1089 PHE cc_start: 0.2802 (m-80) cc_final: 0.1725 (m-80) REVERT: C 1106 GLN cc_start: 0.1489 (OUTLIER) cc_final: -0.0637 (mp10) REVERT: C 1111 GLU cc_start: 0.0312 (tt0) cc_final: 0.0034 (mm-30) REVERT: G 34 MET cc_start: 0.1663 (tpp) cc_final: 0.1414 (tpp) REVERT: J 35 ASN cc_start: -0.2174 (OUTLIER) cc_final: -0.2888 (t0) REVERT: J 109 TRP cc_start: 0.0241 (p90) cc_final: -0.0239 (p90) REVERT: K 97 LEU cc_start: -0.0444 (mt) cc_final: -0.0945 (mt) outliers start: 70 outliers final: 42 residues processed: 195 average time/residue: 0.3835 time to fit residues: 125.0451 Evaluate side-chains 178 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 2.773 ------------------------------------------------------------------------------- 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 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 877 LEU 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 1004 LEU 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 286 THR Chi-restraints excluded: chain B residue 317 ASN 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 731 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 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 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 87 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 300 optimal weight: 9.9990 chunk 152 optimal weight: 0.0270 chunk 94 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 314 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** 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 = 0.5334 r_free = 0.5334 target = 0.299454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.5257 r_free = 0.5257 target = 0.291090 restraints weight = 65377.693| |-----------------------------------------------------------------------------| r_work (start): 0.5252 rms_B_bonded: 1.41 r_work: 0.5150 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.5150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1188 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29741 Z= 0.120 Angle : 0.622 13.739 40566 Z= 0.304 Chirality : 0.047 0.870 4694 Planarity : 0.004 0.073 5183 Dihedral : 6.598 93.738 4826 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.28 % Allowed : 17.95 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3626 helix: 0.94 (0.21), residues: 613 sheet: -0.38 (0.17), residues: 935 loop : -1.39 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 36 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.001 PHE C 377 TYR 0.020 0.001 TYR C 351 ARG 0.004 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 32) link_NAG-ASN : angle 2.92967 ( 96) link_BETA1-4 : bond 0.00569 ( 5) link_BETA1-4 : angle 2.71895 ( 15) hydrogen bonds : bond 0.03885 ( 1048) hydrogen bonds : angle 5.60695 ( 2931) SS BOND : bond 0.00377 ( 44) SS BOND : angle 1.10819 ( 88) covalent geometry : bond 0.00260 (29660) covalent geometry : angle 0.60288 (40367) *********************** 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 202 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.2121 (OUTLIER) cc_final: 0.1029 (m) REVERT: A 220 PHE cc_start: 0.0285 (t80) cc_final: -0.0222 (p90) REVERT: A 400 PHE cc_start: 0.2941 (OUTLIER) cc_final: 0.2280 (p90) REVERT: A 451 TYR cc_start: 0.0376 (m-80) cc_final: -0.0247 (m-80) REVERT: A 762 GLN cc_start: 0.3208 (mm-40) cc_final: 0.2162 (tp40) REVERT: A 779 GLN cc_start: 0.0078 (OUTLIER) cc_final: -0.0537 (mt0) REVERT: A 1029 MET cc_start: -0.1086 (ttt) cc_final: -0.1801 (mtp) REVERT: A 1091 ARG cc_start: 0.3106 (mtp85) cc_final: 0.2765 (mmt90) REVERT: B 313 TYR cc_start: 0.2836 (m-80) cc_final: 0.0876 (t80) REVERT: B 318 PHE cc_start: -0.0240 (OUTLIER) cc_final: -0.1320 (p90) REVERT: B 714 ILE cc_start: -0.1609 (OUTLIER) cc_final: -0.2210 (mt) REVERT: B 905 ARG cc_start: -0.0659 (OUTLIER) cc_final: -0.1219 (mtt-85) REVERT: B 1072 GLU cc_start: 0.1844 (OUTLIER) cc_final: 0.0437 (mm-30) REVERT: C 364 ASP cc_start: 0.2199 (t0) cc_final: 0.1182 (p0) REVERT: C 432 CYS cc_start: 0.0704 (OUTLIER) cc_final: 0.0365 (p) REVERT: C 988 GLU cc_start: 0.0164 (OUTLIER) cc_final: -0.0263 (tp30) REVERT: C 1086 LYS cc_start: 0.4378 (OUTLIER) cc_final: 0.3550 (mtmm) REVERT: C 1089 PHE cc_start: 0.3122 (m-80) cc_final: 0.1957 (m-80) REVERT: C 1106 GLN cc_start: 0.1428 (OUTLIER) cc_final: -0.0853 (mp10) REVERT: G 34 MET cc_start: 0.1682 (tpp) cc_final: 0.1376 (tpp) REVERT: J 109 TRP cc_start: 0.0433 (p90) cc_final: -0.0122 (p90) REVERT: K 97 LEU cc_start: -0.0237 (mt) cc_final: -0.0694 (mt) outliers start: 71 outliers final: 47 residues processed: 197 average time/residue: 0.3877 time to fit residues: 126.4389 Evaluate side-chains 185 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 127 time to evaluate : 3.010 ------------------------------------------------------------------------------- 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 245 HIS Chi-restraints excluded: chain A residue 266 TYR 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 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR 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 1004 LEU 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 286 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 805 ILE Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE 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 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 233 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 318 optimal weight: 0.3980 chunk 328 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 298 optimal weight: 0.0670 chunk 98 optimal weight: 0.0270 chunk 258 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 777 ASN B 949 GLN ** K 36 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 = 0.5333 r_free = 0.5333 target = 0.299185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.5253 r_free = 0.5253 target = 0.290476 restraints weight = 64951.142| |-----------------------------------------------------------------------------| r_work (start): 0.5253 rms_B_bonded: 1.43 r_work: 0.5149 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.5149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1153 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 29741 Z= 0.109 Angle : 0.586 10.973 40566 Z= 0.288 Chirality : 0.045 0.431 4694 Planarity : 0.004 0.068 5183 Dihedral : 6.605 120.941 4826 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.18 % Allowed : 18.01 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3626 helix: 1.12 (0.22), residues: 607 sheet: -0.34 (0.17), residues: 930 loop : -1.31 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 36 HIS 0.003 0.001 HIS A1048 PHE 0.024 0.001 PHE C 377 TYR 0.019 0.001 TYR C 351 ARG 0.004 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 32) link_NAG-ASN : angle 2.53491 ( 96) link_BETA1-4 : bond 0.00441 ( 5) link_BETA1-4 : angle 3.03273 ( 15) hydrogen bonds : bond 0.03666 ( 1048) hydrogen bonds : angle 5.41879 ( 2931) SS BOND : bond 0.00433 ( 44) SS BOND : angle 1.16631 ( 88) covalent geometry : bond 0.00238 (29660) covalent geometry : angle 0.56822 (40367) *********************** 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 209 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 2.942 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.2056 (OUTLIER) cc_final: 0.0834 (m) REVERT: A 64 TRP cc_start: 0.4058 (t60) cc_final: 0.3627 (t60) REVERT: A 220 PHE cc_start: 0.0299 (t80) cc_final: -0.0144 (p90) REVERT: A 278 LYS cc_start: 0.2297 (tmtt) cc_final: 0.1928 (mmtt) REVERT: A 400 PHE cc_start: 0.2998 (OUTLIER) cc_final: 0.2360 (p90) REVERT: A 451 TYR cc_start: 0.0240 (m-80) cc_final: -0.0393 (m-80) REVERT: A 762 GLN cc_start: 0.3224 (mm-40) cc_final: 0.2164 (tp40) REVERT: A 779 GLN cc_start: -0.0068 (OUTLIER) cc_final: -0.0700 (mt0) REVERT: A 1029 MET cc_start: -0.1237 (ttt) cc_final: -0.1588 (mtp) REVERT: A 1091 ARG cc_start: 0.3142 (mtp85) cc_final: 0.2430 (mpt-90) REVERT: B 228 ASP cc_start: 0.1185 (OUTLIER) cc_final: 0.0571 (m-30) REVERT: B 313 TYR cc_start: 0.2966 (m-80) cc_final: 0.1492 (m-80) REVERT: B 318 PHE cc_start: -0.0190 (OUTLIER) cc_final: -0.0714 (t80) REVERT: B 386 LYS cc_start: -0.0410 (ptpt) cc_final: -0.0685 (mtmt) REVERT: B 697 MET cc_start: -0.0362 (mtt) cc_final: -0.2566 (mtp) REVERT: B 714 ILE cc_start: -0.1437 (OUTLIER) cc_final: -0.2177 (mt) REVERT: C 364 ASP cc_start: 0.2080 (t0) cc_final: 0.1178 (p0) REVERT: C 432 CYS cc_start: 0.0769 (OUTLIER) cc_final: 0.0431 (p) REVERT: C 988 GLU cc_start: 0.0145 (OUTLIER) cc_final: -0.0779 (tm-30) REVERT: C 1089 PHE cc_start: 0.3335 (m-80) cc_final: 0.2298 (m-80) REVERT: C 1106 GLN cc_start: 0.1374 (OUTLIER) cc_final: -0.0752 (mp10) REVERT: G 34 MET cc_start: 0.1667 (tpp) cc_final: 0.1386 (tpp) REVERT: J 35 ASN cc_start: -0.2231 (OUTLIER) cc_final: -0.2587 (t0) REVERT: J 109 TRP cc_start: 0.0194 (p90) cc_final: -0.0375 (t60) REVERT: K 95 GLN cc_start: 0.1673 (pp30) cc_final: -0.1481 (pt0) REVERT: K 97 LEU cc_start: -0.0398 (mt) cc_final: -0.1267 (mt) outliers start: 68 outliers final: 50 residues processed: 203 average time/residue: 0.4026 time to fit residues: 135.7678 Evaluate side-chains 190 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 130 time to evaluate : 2.881 ------------------------------------------------------------------------------- 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 266 TYR 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 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR 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 1004 LEU 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 228 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1116 THR 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 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1125 ASN 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 E residue 42 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 40 optimal weight: 1.9990 chunk 324 optimal weight: 0.9980 chunk 79 optimal weight: 0.0270 chunk 212 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 325 optimal weight: 30.0000 chunk 135 optimal weight: 0.3980 chunk 23 optimal weight: 0.0060 chunk 75 optimal weight: 0.7980 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN C 965 GLN ** K 36 ASN ** 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 = 0.5334 r_free = 0.5334 target = 0.299139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.5256 r_free = 0.5256 target = 0.290648 restraints weight = 64748.821| |-----------------------------------------------------------------------------| r_work (start): 0.5256 rms_B_bonded: 1.43 r_work: 0.5144 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.5144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1145 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 29741 Z= 0.104 Angle : 0.580 11.041 40566 Z= 0.286 Chirality : 0.045 0.453 4694 Planarity : 0.004 0.067 5183 Dihedral : 6.295 110.187 4826 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.25 % Allowed : 18.01 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3626 helix: 1.22 (0.22), residues: 608 sheet: -0.29 (0.17), residues: 921 loop : -1.29 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 36 HIS 0.003 0.001 HIS A1048 PHE 0.056 0.001 PHE B 306 TYR 0.019 0.001 TYR C 351 ARG 0.004 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 32) link_NAG-ASN : angle 2.55978 ( 96) link_BETA1-4 : bond 0.00424 ( 5) link_BETA1-4 : angle 3.05972 ( 15) hydrogen bonds : bond 0.03560 ( 1048) hydrogen bonds : angle 5.32524 ( 2931) SS BOND : bond 0.00319 ( 44) SS BOND : angle 1.42760 ( 88) covalent geometry : bond 0.00228 (29660) covalent geometry : angle 0.56102 (40367) ********************** 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 203 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 133 time to evaluate : 3.041 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.2024 (OUTLIER) cc_final: 0.0803 (m) REVERT: A 64 TRP cc_start: 0.4176 (t60) cc_final: 0.3691 (t60) REVERT: A 220 PHE cc_start: 0.0305 (t80) cc_final: -0.0108 (p90) REVERT: A 278 LYS cc_start: 0.2306 (tmtt) cc_final: 0.1976 (mmtt) REVERT: A 400 PHE cc_start: 0.3004 (OUTLIER) cc_final: 0.2276 (p90) REVERT: A 451 TYR cc_start: 0.0448 (m-80) cc_final: -0.0195 (m-80) REVERT: A 762 GLN cc_start: 0.3222 (mm-40) cc_final: 0.2166 (tp40) REVERT: A 779 GLN cc_start: -0.0302 (OUTLIER) cc_final: -0.0628 (mt0) REVERT: A 1029 MET cc_start: -0.1414 (ttt) cc_final: -0.1696 (mtp) REVERT: A 1091 ARG cc_start: 0.3092 (mtp85) cc_final: 0.2036 (mpt-90) REVERT: B 228 ASP cc_start: 0.1139 (OUTLIER) cc_final: 0.0510 (m-30) REVERT: B 313 TYR cc_start: 0.3018 (m-80) cc_final: 0.1551 (m-80) REVERT: B 386 LYS cc_start: -0.0500 (ptpt) cc_final: -0.0770 (mtmt) REVERT: B 697 MET cc_start: -0.0267 (mtt) cc_final: -0.1958 (mtp) REVERT: B 714 ILE cc_start: -0.1600 (OUTLIER) cc_final: -0.2253 (mt) REVERT: C 126 VAL cc_start: 0.1921 (t) cc_final: 0.1709 (p) REVERT: C 364 ASP cc_start: 0.2006 (t0) cc_final: 0.1146 (p0) REVERT: C 432 CYS cc_start: 0.0813 (OUTLIER) cc_final: 0.0532 (p) REVERT: C 784 GLN cc_start: 0.0096 (mt0) cc_final: -0.0269 (pt0) REVERT: C 988 GLU cc_start: 0.0149 (OUTLIER) cc_final: -0.0809 (tm-30) REVERT: C 1089 PHE cc_start: 0.3342 (m-80) cc_final: 0.2239 (m-80) REVERT: C 1106 GLN cc_start: 0.1465 (OUTLIER) cc_final: -0.0792 (mp10) REVERT: G 34 MET cc_start: 0.1603 (tpp) cc_final: 0.1324 (tpp) REVERT: J 35 ASN cc_start: -0.2205 (OUTLIER) cc_final: -0.2869 (t0) REVERT: J 109 TRP cc_start: 0.0350 (p90) cc_final: 0.0058 (p90) REVERT: K 95 GLN cc_start: 0.1837 (pp30) cc_final: -0.0981 (pt0) REVERT: K 97 LEU cc_start: -0.0380 (mt) cc_final: -0.1255 (mt) outliers start: 70 outliers final: 54 residues processed: 195 average time/residue: 0.3851 time to fit residues: 124.9770 Evaluate side-chains 191 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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 266 TYR 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 592 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR 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 1004 LEU 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 228 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1116 THR 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 432 CYS Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 94 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 16 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 335 optimal weight: 40.0000 chunk 308 optimal weight: 10.0000 chunk 358 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 350 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.298003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.296487 restraints weight = 69760.697| |-----------------------------------------------------------------------------| r_work (start): 0.5312 rms_B_bonded: 0.29 r_work: 0.5279 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.5239 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.5239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1467 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.213 29741 Z= 0.296 Angle : 0.990 22.756 40566 Z= 0.494 Chirality : 0.058 0.561 4694 Planarity : 0.007 0.085 5183 Dihedral : 8.336 106.488 4826 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 2.54 % Allowed : 17.82 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3626 helix: -0.40 (0.20), residues: 615 sheet: -0.74 (0.17), residues: 865 loop : -1.63 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 886 HIS 0.016 0.002 HIS A1048 PHE 0.046 0.003 PHE B 797 TYR 0.044 0.003 TYR A1067 ARG 0.011 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.01157 ( 32) link_NAG-ASN : angle 3.62858 ( 96) link_BETA1-4 : bond 0.00580 ( 5) link_BETA1-4 : angle 3.31449 ( 15) hydrogen bonds : bond 0.06517 ( 1048) hydrogen bonds : angle 6.97195 ( 2931) SS BOND : bond 0.00514 ( 44) SS BOND : angle 1.92599 ( 88) covalent geometry : bond 0.00675 (29660) covalent geometry : angle 0.97063 (40367) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13285.74 seconds wall clock time: 234 minutes 12.22 seconds (14052.22 seconds total)