Starting phenix.real_space_refine on Fri Jun 27 00:11:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz6_26880/06_2025/7uz6_26880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz6_26880/06_2025/7uz6_26880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz6_26880/06_2025/7uz6_26880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz6_26880/06_2025/7uz6_26880.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz6_26880/06_2025/7uz6_26880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz6_26880/06_2025/7uz6_26880.cif" } resolution = 2.8 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= -0.001 sd= 0.029 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 132 5.16 5 C 19689 2.51 5 N 5106 2.21 5 O 6015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30942 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "P" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "Q" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.70, per 1000 atoms: 0.54 Number of scatterers: 30942 At special positions: 0 Unit cell: (153.088, 151.424, 189.696, 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 132 16.00 O 6015 8.00 N 5106 7.00 C 19689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " 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 NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B 234 " " NAG B1313 " - " ASN B 282 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 717 " " NAG C1312 " - " ASN C 234 " " NAG C1313 " - " ASN C 282 " Time building additional restraints: 6.99 Conformation dependent library (CDL) restraints added in 3.7 seconds 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7302 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 71 sheets defined 21.1% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.724A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.263A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.302A 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 438 through 443 Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.619A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.591A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.472A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.631A pdb=" N THR B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.136A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.553A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.732A 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: 3.588A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.212A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.578A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.609A pdb=" N THR C 250 " --> pdb=" O ARG C 246 " (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 364 through 371 removed outlier: 4.131A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.667A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.876A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.521A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.096A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.499A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.461A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 4.090A pdb=" N TYR H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 4.129A pdb=" N ILE L 99 " --> pdb=" O SER L 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 37 Processing helix chain 'N' and resid 95 through 100 removed outlier: 3.504A pdb=" N ILE N 99 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA N 100 " --> pdb=" O GLU N 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 removed outlier: 3.564A pdb=" N SER P 99 " --> pdb=" O SER P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.739A pdb=" N ILE Q 99 " --> pdb=" O SER Q 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.898A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.899A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.965A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.956A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 146 removed outlier: 7.036A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.236A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.805A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.628A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.723A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.587A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.603A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.495A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.495A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.881A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.584A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.042A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.781A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.542A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.540A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.209A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.711A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.731A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.614A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.740A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.003A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.161A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.760A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.201A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.711A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.706A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.539A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.652A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.196A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.575A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.489A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.489A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF8, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AF9, first strand: chain 'H' and resid 64 through 67 removed outlier: 3.585A pdb=" N PHE H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 64 through 67 removed outlier: 3.585A pdb=" N PHE H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.952A pdb=" N ASP L 86 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER L 83 " --> pdb=" O ASP L 86 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.591A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.789A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG L 51 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.613A pdb=" N THR M 77 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 65 through 67 removed outlier: 6.897A pdb=" N TRP M 41 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP M 55 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE M 39 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.576A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.576A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP N 86 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 83 " --> pdb=" O ASP N 86 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'N' and resid 66 through 67 removed outlier: 6.851A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS N 55 " --> pdb=" O ILE N 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE N 39 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain 'P' and resid 64 through 67 removed outlier: 3.505A pdb=" N PHE P 64 " --> pdb=" O TYR P 57 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR P 66 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP P 41 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASP P 55 " --> pdb=" O ILE P 39 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE P 39 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL P 42 " --> pdb=" O TYR P 103 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.589A pdb=" N THR Q 5 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Q 24 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL Q 19 " --> pdb=" O ILE Q 91 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.589A pdb=" N THR Q 5 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Q 24 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP Q 86 " --> pdb=" O SER Q 83 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER Q 83 " --> pdb=" O ASP Q 86 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.502A pdb=" N LEU Q 11 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE Q 39 " --> pdb=" O LYS Q 55 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS Q 55 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.502A pdb=" N LEU Q 11 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3171 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: 15.19 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9921 1.35 - 1.47: 8210 1.47 - 1.59: 13386 1.59 - 1.72: 1 1.72 - 1.84: 168 Bond restraints: 31686 Sorted by residual: bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" CB PRO B 230 " pdb=" CG PRO B 230 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.56e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 ... (remaining 31681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 41670 1.35 - 2.70: 1205 2.70 - 4.06: 262 4.06 - 5.41: 37 5.41 - 6.76: 8 Bond angle restraints: 43182 Sorted by residual: angle pdb=" N VAL B 127 " pdb=" CA VAL B 127 " pdb=" C VAL B 127 " ideal model delta sigma weight residual 106.21 110.32 -4.11 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N VAL A 127 " pdb=" CA VAL A 127 " pdb=" C VAL A 127 " ideal model delta sigma weight residual 106.21 110.05 -3.84 1.07e+00 8.73e-01 1.29e+01 angle pdb=" N GLY A1124 " pdb=" CA GLY A1124 " pdb=" C GLY A1124 " ideal model delta sigma weight residual 111.21 114.92 -3.71 1.04e+00 9.25e-01 1.28e+01 angle pdb=" C ARG A 102 " pdb=" N GLY A 103 " pdb=" CA GLY A 103 " ideal model delta sigma weight residual 122.03 117.66 4.37 1.28e+00 6.10e-01 1.17e+01 angle pdb=" N GLY C1124 " pdb=" CA GLY C1124 " pdb=" C GLY C1124 " ideal model delta sigma weight residual 111.21 114.74 -3.53 1.04e+00 9.25e-01 1.15e+01 ... (remaining 43177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.76: 18175 22.76 - 45.52: 954 45.52 - 68.28: 101 68.28 - 91.04: 36 91.04 - 113.79: 3 Dihedral angle restraints: 19269 sinusoidal: 7902 harmonic: 11367 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -24.51 -61.49 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 153.52 -60.52 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -34.74 -51.26 1 1.00e+01 1.00e-02 3.59e+01 ... (remaining 19266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4290 0.065 - 0.130: 664 0.130 - 0.195: 8 0.195 - 0.260: 3 0.260 - 0.325: 6 Chirality restraints: 4971 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 4968 not shown) Planarity restraints: 5583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 49 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO L 50 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 49 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO N 50 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO N 50 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 50 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.015 2.00e-02 2.50e+03 1.52e-02 4.07e+00 pdb=" CG PHE A 906 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.002 2.00e-02 2.50e+03 ... (remaining 5580 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 315 2.62 - 3.19: 27230 3.19 - 3.76: 47629 3.76 - 4.33: 67680 4.33 - 4.90: 113970 Nonbonded interactions: 256824 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.055 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.199 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A 155 " pdb=" NH1 ARG A 246 " model vdw 2.209 3.120 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.212 3.040 ... (remaining 256819 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 70.790 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.170 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: 0.000 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.004 0.107 31767 Z= 0.170 Angle : 0.592 11.991 43383 Z= 0.307 Chirality : 0.045 0.325 4971 Planarity : 0.004 0.096 5544 Dihedral : 13.209 113.795 11841 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.38 (0.13), residues: 3864 helix: 1.46 (0.20), residues: 731 sheet: -0.08 (0.16), residues: 1004 loop : -0.95 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 258 HIS 0.004 0.001 HIS A 625 PHE 0.035 0.001 PHE A 906 TYR 0.021 0.001 TYR B 636 ARG 0.008 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 39) link_NAG-ASN : angle 3.49979 ( 117) hydrogen bonds : bond 0.20173 ( 1131) hydrogen bonds : angle 8.74157 ( 3171) SS BOND : bond 0.00389 ( 42) SS BOND : angle 0.90044 ( 84) covalent geometry : bond 0.00372 (31686) covalent geometry : angle 0.56344 (43182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 3.020 Fit side-chains REVERT: A 153 MET cc_start: 0.7049 (tpt) cc_final: 0.6755 (ptt) REVERT: A 495 TYR cc_start: 0.6814 (t80) cc_final: 0.6544 (t80) REVERT: A 1123 SER cc_start: 0.8614 (m) cc_final: 0.8340 (m) REVERT: B 463 PRO cc_start: 0.8981 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: H 89 MET cc_start: 0.4529 (ppp) cc_final: 0.3804 (ppp) REVERT: M 21 MET cc_start: 0.6675 (mmt) cc_final: 0.6117 (mpt) REVERT: M 43 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6879 (ttmm) REVERT: N 91 ILE cc_start: 0.6764 (mt) cc_final: 0.6549 (pt) REVERT: P 21 MET cc_start: 0.6663 (mmt) cc_final: 0.6179 (mpt) REVERT: P 89 MET cc_start: 0.4287 (ppp) cc_final: 0.3850 (ppp) REVERT: P 108 ASP cc_start: 0.7173 (t70) cc_final: 0.6951 (t70) REVERT: P 113 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7157 (ptp-110) outliers start: 1 outliers final: 2 residues processed: 377 average time/residue: 1.2886 time to fit residues: 582.9823 Evaluate side-chains 264 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 10.0000 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 0.0370 chunk 155 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 348 optimal weight: 10.0000 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 422 ASN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN H 36 HIS L 6 GLN L 108 ASN N 108 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.197865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120345 restraints weight = 38547.188| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.61 r_work: 0.3348 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31767 Z= 0.175 Angle : 0.610 12.471 43383 Z= 0.308 Chirality : 0.047 0.329 4971 Planarity : 0.005 0.070 5544 Dihedral : 6.505 96.661 5020 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.31 % Allowed : 7.21 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.31 (0.13), residues: 3864 helix: 1.84 (0.20), residues: 682 sheet: -0.13 (0.16), residues: 1002 loop : -0.91 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.005 0.001 HIS A 49 PHE 0.024 0.001 PHE A 906 TYR 0.033 0.002 TYR H 109 ARG 0.009 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00782 ( 39) link_NAG-ASN : angle 3.59042 ( 117) hydrogen bonds : bond 0.04611 ( 1131) hydrogen bonds : angle 6.61623 ( 3171) SS BOND : bond 0.00474 ( 42) SS BOND : angle 0.95535 ( 84) covalent geometry : bond 0.00416 (31686) covalent geometry : angle 0.58021 (43182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 303 time to evaluate : 3.565 Fit side-chains REVERT: A 153 MET cc_start: 0.7234 (tpt) cc_final: 0.6658 (ptt) REVERT: A 495 TYR cc_start: 0.6882 (t80) cc_final: 0.6634 (t80) REVERT: B 463 PRO cc_start: 0.8743 (Cg_exo) cc_final: 0.8383 (Cg_endo) REVERT: C 153 MET cc_start: 0.6844 (pp-130) cc_final: 0.5719 (pmm) REVERT: C 290 ASP cc_start: 0.7694 (t0) cc_final: 0.7454 (t0) REVERT: C 309 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: C 994 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8077 (t0) REVERT: H 89 MET cc_start: 0.3875 (ppp) cc_final: 0.3440 (ppp) REVERT: L 71 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7710 (mp) REVERT: M 21 MET cc_start: 0.5842 (mmt) cc_final: 0.5405 (mpt) REVERT: M 40 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7883 (p) REVERT: M 113 ARG cc_start: 0.7687 (mpp-170) cc_final: 0.6893 (ptp-110) REVERT: N 27 GLN cc_start: 0.7855 (mp-120) cc_final: 0.7554 (mp-120) REVERT: P 21 MET cc_start: 0.6081 (mmt) cc_final: 0.5443 (mmm) REVERT: P 41 TRP cc_start: 0.5346 (m100) cc_final: 0.5068 (m100) REVERT: P 89 MET cc_start: 0.4065 (ppp) cc_final: 0.3814 (ppp) REVERT: P 108 ASP cc_start: 0.7202 (t70) cc_final: 0.6947 (t70) REVERT: Q 39 ILE cc_start: 0.7765 (mm) cc_final: 0.7555 (mm) REVERT: Q 42 TYR cc_start: 0.6274 (m-10) cc_final: 0.5998 (m-10) outliers start: 44 outliers final: 19 residues processed: 322 average time/residue: 1.1911 time to fit residues: 468.5749 Evaluate side-chains 303 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 97 optimal weight: 0.5980 chunk 366 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 236 optimal weight: 40.0000 chunk 376 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 354 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS N 108 ASN P 44 GLN Q 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.199094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121891 restraints weight = 38641.974| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.61 r_work: 0.3365 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31767 Z= 0.128 Angle : 0.564 12.598 43383 Z= 0.282 Chirality : 0.045 0.330 4971 Planarity : 0.004 0.063 5544 Dihedral : 6.036 93.545 5016 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.70 % Allowed : 10.04 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.23 (0.13), residues: 3864 helix: 2.07 (0.20), residues: 682 sheet: -0.23 (0.15), residues: 1044 loop : -0.84 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 38 HIS 0.005 0.001 HIS A 625 PHE 0.017 0.001 PHE A 906 TYR 0.034 0.001 TYR M 109 ARG 0.010 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 39) link_NAG-ASN : angle 3.51502 ( 117) hydrogen bonds : bond 0.04034 ( 1131) hydrogen bonds : angle 6.14651 ( 3171) SS BOND : bond 0.00375 ( 42) SS BOND : angle 0.86355 ( 84) covalent geometry : bond 0.00296 (31686) covalent geometry : angle 0.53375 (43182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 3.541 Fit side-chains REVERT: A 153 MET cc_start: 0.7121 (tpt) cc_final: 0.6618 (ptt) REVERT: A 177 MET cc_start: 0.6073 (ppp) cc_final: 0.5832 (ppp) REVERT: A 290 ASP cc_start: 0.7493 (t0) cc_final: 0.7205 (t0) REVERT: A 357 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7944 (ptm160) REVERT: A 495 TYR cc_start: 0.6867 (t80) cc_final: 0.6604 (t80) REVERT: A 574 ASP cc_start: 0.7785 (t0) cc_final: 0.7422 (t0) REVERT: A 1092 GLU cc_start: 0.8207 (tp30) cc_final: 0.7178 (pt0) REVERT: C 153 MET cc_start: 0.6926 (pp-130) cc_final: 0.5725 (pmm) REVERT: C 309 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: C 357 ARG cc_start: 0.8559 (ptm160) cc_final: 0.8354 (ptm160) REVERT: C 615 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7908 (m) REVERT: C 994 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8059 (t0) REVERT: C 1092 GLU cc_start: 0.8318 (tp30) cc_final: 0.7550 (pt0) REVERT: H 21 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5278 (mpt) REVERT: H 89 MET cc_start: 0.3899 (ppp) cc_final: 0.3148 (ppp) REVERT: L 42 TYR cc_start: 0.5777 (m-80) cc_final: 0.5356 (m-80) REVERT: M 21 MET cc_start: 0.5833 (mmt) cc_final: 0.5444 (mpt) REVERT: M 40 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7952 (p) REVERT: M 43 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6762 (ttmm) REVERT: M 113 ARG cc_start: 0.7791 (mpp-170) cc_final: 0.7036 (ptp-110) REVERT: N 27 GLN cc_start: 0.7819 (mp-120) cc_final: 0.7541 (mp-120) REVERT: N 39 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7477 (mm) REVERT: P 21 MET cc_start: 0.6009 (mmt) cc_final: 0.5511 (mmm) REVERT: P 89 MET cc_start: 0.4005 (ppp) cc_final: 0.3767 (ppp) REVERT: P 108 ASP cc_start: 0.7170 (t70) cc_final: 0.6944 (t70) REVERT: Q 39 ILE cc_start: 0.7818 (mm) cc_final: 0.7604 (mm) REVERT: Q 42 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.6057 (m-10) outliers start: 57 outliers final: 19 residues processed: 325 average time/residue: 1.1543 time to fit residues: 461.6772 Evaluate side-chains 307 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain Q residue 42 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 50 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 314 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN H 36 HIS L 108 ASN N 108 ASN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.198532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121356 restraints weight = 38581.340| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.60 r_work: 0.3357 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31767 Z= 0.141 Angle : 0.566 12.431 43383 Z= 0.281 Chirality : 0.045 0.330 4971 Planarity : 0.004 0.059 5544 Dihedral : 5.837 90.055 5016 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.09 % Allowed : 10.99 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.21 (0.13), residues: 3864 helix: 2.10 (0.20), residues: 688 sheet: -0.15 (0.16), residues: 1035 loop : -0.88 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.004 0.001 HIS A 625 PHE 0.019 0.001 PHE H 64 TYR 0.028 0.001 TYR H 109 ARG 0.011 0.001 ARG M 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00737 ( 39) link_NAG-ASN : angle 3.50750 ( 117) hydrogen bonds : bond 0.03874 ( 1131) hydrogen bonds : angle 5.96105 ( 3171) SS BOND : bond 0.00440 ( 42) SS BOND : angle 0.83021 ( 84) covalent geometry : bond 0.00334 (31686) covalent geometry : angle 0.53605 (43182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 290 time to evaluate : 3.781 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6995 (tpt) cc_final: 0.6542 (ptt) REVERT: A 177 MET cc_start: 0.5999 (ppp) cc_final: 0.5683 (ppp) REVERT: A 357 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7735 (ptm160) REVERT: A 564 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: A 574 ASP cc_start: 0.7819 (t0) cc_final: 0.7380 (t0) REVERT: A 1092 GLU cc_start: 0.8217 (tp30) cc_final: 0.7193 (pt0) REVERT: B 534 VAL cc_start: 0.8191 (t) cc_final: 0.7907 (m) REVERT: C 153 MET cc_start: 0.6850 (pp-130) cc_final: 0.5698 (pmm) REVERT: C 177 MET cc_start: 0.5830 (mtp) cc_final: 0.5530 (mpp) REVERT: C 495 TYR cc_start: 0.7079 (t80) cc_final: 0.6527 (t80) REVERT: C 574 ASP cc_start: 0.7636 (t0) cc_final: 0.7428 (t0) REVERT: C 615 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7937 (m) REVERT: C 1092 GLU cc_start: 0.8326 (tp30) cc_final: 0.7543 (pt0) REVERT: H 21 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5173 (mpt) REVERT: H 43 LYS cc_start: 0.7429 (ttpp) cc_final: 0.7104 (ttmm) REVERT: H 89 MET cc_start: 0.3903 (ppp) cc_final: 0.3212 (ppp) REVERT: L 42 TYR cc_start: 0.5874 (m-80) cc_final: 0.5502 (m-80) REVERT: M 21 MET cc_start: 0.5790 (mmt) cc_final: 0.5455 (mpt) REVERT: M 43 LYS cc_start: 0.7092 (ttpp) cc_final: 0.6719 (ttmm) REVERT: M 113 ARG cc_start: 0.7800 (mpp-170) cc_final: 0.7119 (ptp-110) REVERT: N 27 GLN cc_start: 0.7829 (mp-120) cc_final: 0.7539 (mp-120) REVERT: N 39 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7463 (mm) REVERT: P 21 MET cc_start: 0.5913 (mmt) cc_final: 0.5432 (mmm) REVERT: P 43 LYS cc_start: 0.7164 (tttt) cc_final: 0.6641 (tmtt) REVERT: P 89 MET cc_start: 0.4164 (ppp) cc_final: 0.3777 (ppp) REVERT: P 108 ASP cc_start: 0.7181 (t70) cc_final: 0.6906 (t70) REVERT: Q 42 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.6076 (m-10) outliers start: 70 outliers final: 30 residues processed: 327 average time/residue: 1.5651 time to fit residues: 634.4499 Evaluate side-chains 308 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 4.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 42 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 334 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 280 optimal weight: 0.4980 chunk 154 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 336 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS L 108 ASN N 108 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.198600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121015 restraints weight = 38654.612| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.57 r_work: 0.3293 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31767 Z= 0.214 Angle : 0.616 12.166 43383 Z= 0.306 Chirality : 0.047 0.334 4971 Planarity : 0.004 0.058 5544 Dihedral : 5.734 69.347 5016 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 2.29 % Allowed : 12.39 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.34 (0.13), residues: 3864 helix: 1.93 (0.20), residues: 681 sheet: -0.30 (0.15), residues: 1060 loop : -0.90 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 38 HIS 0.005 0.001 HIS A 625 PHE 0.024 0.002 PHE H 64 TYR 0.025 0.002 TYR H 109 ARG 0.010 0.001 ARG M 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 39) link_NAG-ASN : angle 3.67830 ( 117) hydrogen bonds : bond 0.04283 ( 1131) hydrogen bonds : angle 5.98393 ( 3171) SS BOND : bond 0.00590 ( 42) SS BOND : angle 1.28844 ( 84) covalent geometry : bond 0.00514 (31686) covalent geometry : angle 0.58391 (43182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 286 time to evaluate : 3.036 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7011 (tpt) cc_final: 0.6573 (ptt) REVERT: A 177 MET cc_start: 0.5943 (ppp) cc_final: 0.5159 (pp-130) REVERT: A 357 ARG cc_start: 0.8373 (ttp80) cc_final: 0.7755 (ptm160) REVERT: A 495 TYR cc_start: 0.6707 (t80) cc_final: 0.6464 (t80) REVERT: A 564 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: A 574 ASP cc_start: 0.7906 (t0) cc_final: 0.7471 (t0) REVERT: A 756 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: C 153 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.5738 (pmm) REVERT: C 495 TYR cc_start: 0.7192 (t80) cc_final: 0.6610 (t80) REVERT: C 1092 GLU cc_start: 0.8406 (tp30) cc_final: 0.7555 (pt0) REVERT: C 1144 GLU cc_start: 0.8620 (mp0) cc_final: 0.8189 (mp0) REVERT: H 39 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.7956 (tp) REVERT: H 43 LYS cc_start: 0.7578 (ttpp) cc_final: 0.7188 (ttmm) REVERT: H 89 MET cc_start: 0.3977 (ppp) cc_final: 0.3751 (ppp) REVERT: L 26 SER cc_start: 0.8245 (t) cc_final: 0.8012 (m) REVERT: L 42 TYR cc_start: 0.6053 (m-80) cc_final: 0.5780 (m-80) REVERT: M 21 MET cc_start: 0.5840 (mmt) cc_final: 0.5529 (mpt) REVERT: M 43 LYS cc_start: 0.7081 (ttpp) cc_final: 0.6681 (ttmm) REVERT: M 64 PHE cc_start: 0.8122 (t80) cc_final: 0.7600 (t80) REVERT: M 113 ARG cc_start: 0.7765 (mpp-170) cc_final: 0.7156 (ptp-110) REVERT: N 27 GLN cc_start: 0.7882 (mp-120) cc_final: 0.7600 (mp-120) REVERT: P 21 MET cc_start: 0.5895 (mmt) cc_final: 0.5221 (mmm) REVERT: P 89 MET cc_start: 0.4069 (ppp) cc_final: 0.3693 (ppp) REVERT: P 108 ASP cc_start: 0.7201 (t70) cc_final: 0.6871 (t70) outliers start: 77 outliers final: 39 residues processed: 327 average time/residue: 1.1507 time to fit residues: 465.8467 Evaluate side-chains 319 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain P residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 73 optimal weight: 0.8980 chunk 310 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 283 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 360 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.201010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123931 restraints weight = 38752.067| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.58 r_work: 0.3361 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31767 Z= 0.126 Angle : 0.571 12.188 43383 Z= 0.282 Chirality : 0.045 0.328 4971 Planarity : 0.004 0.055 5544 Dihedral : 5.425 58.177 5016 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 2.14 % Allowed : 13.35 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.19 (0.13), residues: 3864 helix: 2.20 (0.20), residues: 673 sheet: -0.16 (0.16), residues: 1021 loop : -0.86 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS A 207 PHE 0.025 0.001 PHE H 64 TYR 0.022 0.001 TYR A 453 ARG 0.012 0.001 ARG M 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00737 ( 39) link_NAG-ASN : angle 3.58469 ( 117) hydrogen bonds : bond 0.03722 ( 1131) hydrogen bonds : angle 5.78336 ( 3171) SS BOND : bond 0.00445 ( 42) SS BOND : angle 0.97874 ( 84) covalent geometry : bond 0.00296 (31686) covalent geometry : angle 0.53896 (43182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 285 time to evaluate : 3.321 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5157 (mmt180) cc_final: 0.4953 (mmt180) REVERT: A 129 LYS cc_start: 0.6901 (tmtt) cc_final: 0.6434 (tptp) REVERT: A 153 MET cc_start: 0.6954 (tpt) cc_final: 0.6558 (ptt) REVERT: A 177 MET cc_start: 0.5983 (ppp) cc_final: 0.5117 (pp-130) REVERT: A 290 ASP cc_start: 0.7609 (t0) cc_final: 0.7272 (t0) REVERT: A 357 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7740 (ptm160) REVERT: A 495 TYR cc_start: 0.6754 (t80) cc_final: 0.6508 (t80) REVERT: A 516 GLU cc_start: 0.8097 (pt0) cc_final: 0.7782 (pm20) REVERT: A 564 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: A 574 ASP cc_start: 0.7834 (t0) cc_final: 0.7477 (t0) REVERT: A 756 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: A 868 GLU cc_start: 0.8121 (tt0) cc_final: 0.7380 (tp30) REVERT: A 1092 GLU cc_start: 0.8285 (tp30) cc_final: 0.7325 (pt0) REVERT: A 1094 VAL cc_start: 0.7613 (OUTLIER) cc_final: 0.7408 (p) REVERT: B 346 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7981 (ttm110) REVERT: B 534 VAL cc_start: 0.8275 (t) cc_final: 0.7899 (m) REVERT: B 661 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7832 (mm-30) REVERT: C 153 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.5694 (pmm) REVERT: C 309 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7755 (mm-30) REVERT: C 495 TYR cc_start: 0.7160 (t80) cc_final: 0.6567 (t80) REVERT: C 868 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: C 1092 GLU cc_start: 0.8271 (tp30) cc_final: 0.7555 (pt0) REVERT: C 1144 GLU cc_start: 0.8628 (mp0) cc_final: 0.8268 (mp0) REVERT: H 39 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.7931 (tp) REVERT: H 43 LYS cc_start: 0.7475 (ttpp) cc_final: 0.7018 (ttmm) REVERT: H 89 MET cc_start: 0.4190 (ppp) cc_final: 0.3705 (ppp) REVERT: L 26 SER cc_start: 0.8294 (t) cc_final: 0.8073 (m) REVERT: L 42 TYR cc_start: 0.6028 (m-80) cc_final: 0.5694 (m-80) REVERT: M 21 MET cc_start: 0.5873 (mmt) cc_final: 0.5521 (mpt) REVERT: M 43 LYS cc_start: 0.7087 (ttpp) cc_final: 0.6700 (ttmm) REVERT: M 64 PHE cc_start: 0.8090 (t80) cc_final: 0.7581 (t80) REVERT: M 113 ARG cc_start: 0.7705 (mpp-170) cc_final: 0.6616 (ptp-110) REVERT: N 26 SER cc_start: 0.8566 (t) cc_final: 0.8348 (m) REVERT: N 27 GLN cc_start: 0.7885 (mp-120) cc_final: 0.7634 (mp10) REVERT: P 21 MET cc_start: 0.5863 (mmt) cc_final: 0.5273 (mmm) REVERT: P 89 MET cc_start: 0.4060 (ppp) cc_final: 0.3624 (ppp) REVERT: P 108 ASP cc_start: 0.7212 (t70) cc_final: 0.6905 (t70) outliers start: 72 outliers final: 32 residues processed: 331 average time/residue: 1.1736 time to fit residues: 473.8270 Evaluate side-chains 312 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain P residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 154 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 358 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 349 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 787 GLN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS L 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.196877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126344 restraints weight = 38804.569| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.95 r_work: 0.3256 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 31767 Z= 0.252 Angle : 0.649 11.818 43383 Z= 0.322 Chirality : 0.048 0.337 4971 Planarity : 0.004 0.048 5544 Dihedral : 5.562 59.919 5016 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 2.41 % Allowed : 13.67 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.39 (0.13), residues: 3864 helix: 1.88 (0.20), residues: 673 sheet: -0.35 (0.16), residues: 1037 loop : -0.90 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 886 HIS 0.006 0.001 HIS A1048 PHE 0.021 0.002 PHE A 906 TYR 0.023 0.002 TYR A1067 ARG 0.013 0.001 ARG M 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 39) link_NAG-ASN : angle 3.79882 ( 117) hydrogen bonds : bond 0.04498 ( 1131) hydrogen bonds : angle 5.95092 ( 3171) SS BOND : bond 0.00745 ( 42) SS BOND : angle 1.14249 ( 84) covalent geometry : bond 0.00612 (31686) covalent geometry : angle 0.61774 (43182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 284 time to evaluate : 3.194 Fit side-chains REVERT: A 129 LYS cc_start: 0.7089 (tmtt) cc_final: 0.6589 (tptp) REVERT: A 153 MET cc_start: 0.6965 (tpt) cc_final: 0.6556 (ptt) REVERT: A 177 MET cc_start: 0.5989 (ppp) cc_final: 0.5142 (pp-130) REVERT: A 233 ILE cc_start: 0.5990 (OUTLIER) cc_final: 0.5574 (mt) REVERT: A 290 ASP cc_start: 0.7662 (t0) cc_final: 0.7323 (t0) REVERT: A 357 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7728 (ptm160) REVERT: A 495 TYR cc_start: 0.6832 (t80) cc_final: 0.6556 (t80) REVERT: A 558 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8271 (mptp) REVERT: A 564 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: A 574 ASP cc_start: 0.7884 (t0) cc_final: 0.7466 (t0) REVERT: A 756 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7288 (m-80) REVERT: B 646 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7465 (ttp80) REVERT: B 661 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7863 (mm-30) REVERT: B 994 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8107 (t0) REVERT: C 153 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.5917 (pmm) REVERT: C 495 TYR cc_start: 0.7257 (t80) cc_final: 0.6668 (t80) REVERT: C 1144 GLU cc_start: 0.8557 (mp0) cc_final: 0.8183 (mp0) REVERT: H 39 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.7923 (tp) REVERT: H 43 LYS cc_start: 0.7502 (ttpp) cc_final: 0.7139 (ttmm) REVERT: H 89 MET cc_start: 0.4274 (ppp) cc_final: 0.3796 (ppp) REVERT: L 26 SER cc_start: 0.8288 (t) cc_final: 0.7995 (m) REVERT: L 42 TYR cc_start: 0.5995 (m-80) cc_final: 0.5745 (m-80) REVERT: L 66 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7842 (mt-10) REVERT: M 21 MET cc_start: 0.5839 (mmt) cc_final: 0.5523 (mpt) REVERT: M 43 LYS cc_start: 0.7088 (ttpp) cc_final: 0.6673 (ttmm) REVERT: M 45 ARG cc_start: 0.8873 (mtp-110) cc_final: 0.8596 (mtp-110) REVERT: M 64 PHE cc_start: 0.8160 (t80) cc_final: 0.7653 (t80) REVERT: M 113 ARG cc_start: 0.7630 (mpp-170) cc_final: 0.6915 (ptp-110) REVERT: P 39 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7477 (mp) REVERT: P 89 MET cc_start: 0.3916 (ppp) cc_final: 0.3418 (ppp) REVERT: P 108 ASP cc_start: 0.7276 (t70) cc_final: 0.6891 (t70) outliers start: 81 outliers final: 44 residues processed: 330 average time/residue: 1.1379 time to fit residues: 464.1639 Evaluate side-chains 318 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 317 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 327 optimal weight: 0.0050 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 371 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.198291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121512 restraints weight = 38330.962| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.62 r_work: 0.3361 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31767 Z= 0.111 Angle : 0.570 11.913 43383 Z= 0.282 Chirality : 0.045 0.327 4971 Planarity : 0.004 0.059 5544 Dihedral : 5.212 59.423 5016 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 1.91 % Allowed : 14.60 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.20 (0.13), residues: 3864 helix: 2.24 (0.20), residues: 672 sheet: -0.29 (0.16), residues: 1041 loop : -0.82 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 38 HIS 0.006 0.001 HIS A 207 PHE 0.017 0.001 PHE P 71 TYR 0.028 0.001 TYR A 453 ARG 0.012 0.001 ARG M 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 39) link_NAG-ASN : angle 3.55334 ( 117) hydrogen bonds : bond 0.03552 ( 1131) hydrogen bonds : angle 5.64995 ( 3171) SS BOND : bond 0.00266 ( 42) SS BOND : angle 0.83116 ( 84) covalent geometry : bond 0.00256 (31686) covalent geometry : angle 0.53936 (43182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 3.431 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7002 (tpt) cc_final: 0.6632 (ptt) REVERT: A 170 TYR cc_start: 0.7238 (t80) cc_final: 0.7002 (t80) REVERT: A 177 MET cc_start: 0.5982 (ppp) cc_final: 0.5046 (pp-130) REVERT: A 357 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7661 (ptm160) REVERT: A 495 TYR cc_start: 0.6750 (t80) cc_final: 0.6499 (t80) REVERT: A 516 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: A 558 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8208 (mptp) REVERT: A 574 ASP cc_start: 0.7782 (t0) cc_final: 0.7532 (t0) REVERT: A 697 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8369 (ptm) REVERT: A 756 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: A 868 GLU cc_start: 0.7989 (tt0) cc_final: 0.7198 (tp30) REVERT: A 902 MET cc_start: 0.8193 (mmt) cc_final: 0.7991 (mmt) REVERT: A 1092 GLU cc_start: 0.8226 (tp30) cc_final: 0.7249 (pt0) REVERT: B 237 ARG cc_start: 0.6489 (mtm-85) cc_final: 0.6144 (mpp80) REVERT: C 153 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.5847 (pmm) REVERT: C 177 MET cc_start: 0.6042 (mtt) cc_final: 0.5566 (mpp) REVERT: C 495 TYR cc_start: 0.7159 (t80) cc_final: 0.6522 (t80) REVERT: C 868 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: C 1092 GLU cc_start: 0.8209 (tp30) cc_final: 0.7480 (pt0) REVERT: C 1094 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7418 (p) REVERT: C 1144 GLU cc_start: 0.8576 (mp0) cc_final: 0.8193 (mp0) REVERT: H 39 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.7921 (tp) REVERT: H 43 LYS cc_start: 0.7270 (ttpp) cc_final: 0.6857 (ttmm) REVERT: H 45 ARG cc_start: 0.8488 (tpp-160) cc_final: 0.8001 (mmt90) REVERT: H 89 MET cc_start: 0.4321 (ppp) cc_final: 0.3773 (ppp) REVERT: L 26 SER cc_start: 0.8305 (t) cc_final: 0.8045 (m) REVERT: L 42 TYR cc_start: 0.5976 (m-80) cc_final: 0.5703 (m-80) REVERT: L 66 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7805 (mt-10) REVERT: M 21 MET cc_start: 0.5818 (mmt) cc_final: 0.5502 (mpt) REVERT: M 43 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6626 (ttmm) REVERT: M 45 ARG cc_start: 0.8858 (mtp-110) cc_final: 0.8638 (mtp-110) REVERT: M 64 PHE cc_start: 0.8100 (t80) cc_final: 0.7607 (t80) REVERT: M 113 ARG cc_start: 0.7547 (mpp-170) cc_final: 0.7004 (ptp-110) REVERT: N 27 GLN cc_start: 0.8204 (mp-120) cc_final: 0.7875 (mp10) REVERT: P 89 MET cc_start: 0.3991 (ppp) cc_final: 0.3424 (ppp) REVERT: P 108 ASP cc_start: 0.7207 (t70) cc_final: 0.6818 (t70) REVERT: P 113 ARG cc_start: 0.7656 (mtm110) cc_final: 0.6658 (ptp-110) outliers start: 64 outliers final: 38 residues processed: 315 average time/residue: 1.1792 time to fit residues: 456.5755 Evaluate side-chains 307 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 21 optimal weight: 40.0000 chunk 329 optimal weight: 20.0000 chunk 280 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 310 optimal weight: 0.3980 chunk 350 optimal weight: 30.0000 chunk 360 optimal weight: 10.0000 chunk 294 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 787 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS L 108 ASN ** Q 108 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 = 0.4336 r_free = 0.4336 target = 0.199249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122295 restraints weight = 38430.237| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.71 r_work: 0.3323 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31767 Z= 0.144 Angle : 0.583 11.962 43383 Z= 0.289 Chirality : 0.046 0.329 4971 Planarity : 0.004 0.059 5544 Dihedral : 5.179 59.244 5016 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.56 % Rotamer: Outliers : 1.91 % Allowed : 15.07 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.25 (0.13), residues: 3864 helix: 2.19 (0.20), residues: 673 sheet: -0.33 (0.16), residues: 1048 loop : -0.84 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 38 HIS 0.006 0.001 HIS A 207 PHE 0.017 0.001 PHE B 168 TYR 0.026 0.001 TYR A 453 ARG 0.013 0.001 ARG M 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 39) link_NAG-ASN : angle 3.55280 ( 117) hydrogen bonds : bond 0.03734 ( 1131) hydrogen bonds : angle 5.64997 ( 3171) SS BOND : bond 0.00380 ( 42) SS BOND : angle 0.88790 ( 84) covalent geometry : bond 0.00342 (31686) covalent geometry : angle 0.55281 (43182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 3.453 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6692 (tmtt) cc_final: 0.6224 (tptp) REVERT: A 153 MET cc_start: 0.7027 (tpt) cc_final: 0.6650 (ptt) REVERT: A 170 TYR cc_start: 0.7173 (t80) cc_final: 0.6928 (t80) REVERT: A 177 MET cc_start: 0.5984 (ppp) cc_final: 0.5067 (pp-130) REVERT: A 357 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7619 (ptm160) REVERT: A 467 ASP cc_start: 0.7444 (t70) cc_final: 0.7016 (t0) REVERT: A 495 TYR cc_start: 0.6751 (t80) cc_final: 0.6494 (t80) REVERT: A 516 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: A 558 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8185 (mptp) REVERT: A 574 ASP cc_start: 0.7690 (t0) cc_final: 0.7443 (t0) REVERT: A 756 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6870 (m-80) REVERT: A 868 GLU cc_start: 0.7917 (tt0) cc_final: 0.7149 (tp30) REVERT: A 902 MET cc_start: 0.8092 (mmt) cc_final: 0.7875 (mmt) REVERT: A 1092 GLU cc_start: 0.8218 (tp30) cc_final: 0.7199 (pt0) REVERT: B 153 MET cc_start: 0.7162 (mmm) cc_final: 0.6920 (mmm) REVERT: C 153 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.5922 (pmm) REVERT: C 177 MET cc_start: 0.6024 (mtt) cc_final: 0.5595 (mpp) REVERT: C 495 TYR cc_start: 0.7121 (t80) cc_final: 0.6515 (t80) REVERT: C 1092 GLU cc_start: 0.8253 (tp30) cc_final: 0.7434 (pt0) REVERT: C 1094 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7367 (p) REVERT: C 1144 GLU cc_start: 0.8518 (mp0) cc_final: 0.8137 (mp0) REVERT: H 21 MET cc_start: 0.4654 (mmm) cc_final: 0.3843 (mmt) REVERT: H 39 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.7937 (tp) REVERT: H 43 LYS cc_start: 0.7320 (ttpp) cc_final: 0.7007 (ttmm) REVERT: H 53 ILE cc_start: 0.6508 (mm) cc_final: 0.6061 (mp) REVERT: H 89 MET cc_start: 0.4347 (ppp) cc_final: 0.3645 (ppp) REVERT: L 26 SER cc_start: 0.8305 (t) cc_final: 0.8043 (m) REVERT: L 42 TYR cc_start: 0.5898 (m-80) cc_final: 0.5633 (m-80) REVERT: L 66 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7779 (mt-10) REVERT: M 21 MET cc_start: 0.5672 (mmt) cc_final: 0.5342 (mpt) REVERT: M 43 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6567 (ttmm) REVERT: M 45 ARG cc_start: 0.8840 (mtp-110) cc_final: 0.8624 (mtp-110) REVERT: M 113 ARG cc_start: 0.7507 (mpp-170) cc_final: 0.6752 (ptp-110) REVERT: N 27 GLN cc_start: 0.8170 (mp-120) cc_final: 0.7873 (mp10) REVERT: P 89 MET cc_start: 0.3887 (ppp) cc_final: 0.3350 (ppp) REVERT: P 108 ASP cc_start: 0.7194 (t70) cc_final: 0.6892 (t70) outliers start: 64 outliers final: 42 residues processed: 304 average time/residue: 1.1636 time to fit residues: 439.8640 Evaluate side-chains 306 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain P residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 367 optimal weight: 10.0000 chunk 180 optimal weight: 0.3980 chunk 289 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 348 optimal weight: 8.9990 chunk 249 optimal weight: 4.9990 chunk 317 optimal weight: 4.9990 chunk 129 optimal weight: 40.0000 chunk 170 optimal weight: 1.9990 chunk 243 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 787 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN ** N 108 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 = 0.4341 r_free = 0.4341 target = 0.199053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122131 restraints weight = 38372.111| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.63 r_work: 0.3368 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31767 Z= 0.112 Angle : 0.566 11.730 43383 Z= 0.281 Chirality : 0.045 0.326 4971 Planarity : 0.004 0.061 5544 Dihedral : 4.994 58.533 5016 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 1.55 % Allowed : 15.46 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.17 (0.13), residues: 3864 helix: 2.35 (0.20), residues: 670 sheet: -0.30 (0.16), residues: 1054 loop : -0.81 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 52 HIS 0.006 0.001 HIS A 207 PHE 0.016 0.001 PHE M 71 TYR 0.026 0.001 TYR A 453 ARG 0.014 0.001 ARG M 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 39) link_NAG-ASN : angle 3.47108 ( 117) hydrogen bonds : bond 0.03459 ( 1131) hydrogen bonds : angle 5.52211 ( 3171) SS BOND : bond 0.00235 ( 42) SS BOND : angle 0.77919 ( 84) covalent geometry : bond 0.00258 (31686) covalent geometry : angle 0.53696 (43182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 3.416 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6928 (tpt) cc_final: 0.6626 (ptt) REVERT: A 170 TYR cc_start: 0.7196 (t80) cc_final: 0.6951 (t80) REVERT: A 177 MET cc_start: 0.6039 (ppp) cc_final: 0.5109 (pp-130) REVERT: A 357 ARG cc_start: 0.8361 (ttp80) cc_final: 0.7687 (ptm160) REVERT: A 467 ASP cc_start: 0.7521 (t70) cc_final: 0.7116 (t0) REVERT: A 495 TYR cc_start: 0.6811 (t80) cc_final: 0.6584 (t80) REVERT: A 516 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: A 558 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8225 (mptp) REVERT: A 574 ASP cc_start: 0.7667 (t0) cc_final: 0.7407 (t0) REVERT: A 756 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: A 868 GLU cc_start: 0.7986 (tt0) cc_final: 0.7253 (tp30) REVERT: A 1092 GLU cc_start: 0.8225 (tp30) cc_final: 0.7284 (pt0) REVERT: B 153 MET cc_start: 0.7170 (mmm) cc_final: 0.6915 (mmm) REVERT: B 237 ARG cc_start: 0.6486 (mtm-85) cc_final: 0.6165 (mpp80) REVERT: B 284 THR cc_start: 0.8315 (m) cc_final: 0.8087 (p) REVERT: B 564 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7842 (tp40) REVERT: B 661 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7814 (mm-30) REVERT: B 1092 GLU cc_start: 0.8344 (tp30) cc_final: 0.7556 (pt0) REVERT: C 153 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.5764 (pmm) REVERT: C 177 MET cc_start: 0.6013 (mtt) cc_final: 0.4979 (pp-130) REVERT: C 495 TYR cc_start: 0.7173 (t80) cc_final: 0.6590 (t80) REVERT: C 1144 GLU cc_start: 0.8579 (mp0) cc_final: 0.8181 (mp0) REVERT: H 21 MET cc_start: 0.4932 (mmm) cc_final: 0.3996 (mmt) REVERT: H 39 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.7642 (mm) REVERT: H 43 LYS cc_start: 0.7436 (ttpp) cc_final: 0.7032 (ttmm) REVERT: H 53 ILE cc_start: 0.6601 (mm) cc_final: 0.6141 (mt) REVERT: H 89 MET cc_start: 0.4368 (ppp) cc_final: 0.3794 (ppp) REVERT: H 113 ARG cc_start: 0.7507 (mpp-170) cc_final: 0.7054 (mpp-170) REVERT: L 26 SER cc_start: 0.8368 (t) cc_final: 0.8112 (m) REVERT: L 27 GLN cc_start: 0.7771 (mp-120) cc_final: 0.7243 (mp10) REVERT: L 42 TYR cc_start: 0.5988 (m-80) cc_final: 0.5697 (m-80) REVERT: L 66 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7870 (mt-10) REVERT: M 21 MET cc_start: 0.5822 (mmt) cc_final: 0.5455 (mpt) REVERT: M 43 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6543 (ttmm) REVERT: M 45 ARG cc_start: 0.8819 (mtp-110) cc_final: 0.8613 (mtp-110) REVERT: M 113 ARG cc_start: 0.7584 (mpp-170) cc_final: 0.6827 (ptp-110) REVERT: N 27 GLN cc_start: 0.8179 (mp-120) cc_final: 0.7943 (mp10) REVERT: P 43 LYS cc_start: 0.6994 (tttt) cc_final: 0.6531 (tmtt) REVERT: P 89 MET cc_start: 0.3992 (ppp) cc_final: 0.3425 (ppp) REVERT: P 108 ASP cc_start: 0.7207 (t70) cc_final: 0.6750 (t70) outliers start: 52 outliers final: 40 residues processed: 298 average time/residue: 1.1348 time to fit residues: 416.1512 Evaluate side-chains 300 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 56 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 325 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 126 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 357 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 300 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN Q 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.201753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.125324 restraints weight = 38232.284| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.70 r_work: 0.3363 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31767 Z= 0.111 Angle : 0.559 11.680 43383 Z= 0.277 Chirality : 0.045 0.328 4971 Planarity : 0.004 0.061 5544 Dihedral : 4.870 56.777 5016 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 1.49 % Allowed : 15.61 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.08 (0.13), residues: 3864 helix: 2.57 (0.20), residues: 652 sheet: -0.24 (0.16), residues: 1032 loop : -0.77 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 52 HIS 0.005 0.001 HIS A 625 PHE 0.029 0.001 PHE M 64 TYR 0.026 0.001 TYR A 453 ARG 0.016 0.001 ARG M 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 39) link_NAG-ASN : angle 3.42865 ( 117) hydrogen bonds : bond 0.03422 ( 1131) hydrogen bonds : angle 5.44773 ( 3171) SS BOND : bond 0.00243 ( 42) SS BOND : angle 0.73750 ( 84) covalent geometry : bond 0.00255 (31686) covalent geometry : angle 0.52981 (43182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30951.23 seconds wall clock time: 530 minutes 52.38 seconds (31852.38 seconds total)