Starting phenix.real_space_refine on Fri Mar 6 10:43:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukm_26584/03_2026/7ukm_26584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukm_26584/03_2026/7ukm_26584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ukm_26584/03_2026/7ukm_26584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukm_26584/03_2026/7ukm_26584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukm_26584/03_2026/7ukm_26584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukm_26584/03_2026/7ukm_26584.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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 135 5.16 5 C 19174 2.51 5 N 4955 2.21 5 O 5881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30145 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7902 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 51, 'TRANS': 960} Chain breaks: 8 Chain: "X" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "Y" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "A" Number of atoms: 7902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7902 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 51, 'TRANS': 960} Chain breaks: 8 Chain: "H" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "L" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "C" Number of atoms: 7902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7902 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 51, 'TRANS': 960} Chain breaks: 8 Chain: "M" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 6.32, per 1000 atoms: 0.21 Number of scatterers: 30145 At special positions: 0 Unit cell: (176.79, 185.09, 172.64, 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 135 16.00 O 5881 8.00 N 4955 7.00 C 19174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.04 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 538 " - pdb=" SG CYS B 590 " 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 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=2.04 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 538 " - pdb=" SG CYS A 590 " 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=2.02 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.04 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 657 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 343 " " NAG A1314 " - " ASN A 603 " " NAG A1315 " - " ASN A 122 " " NAG A1316 " - " ASN A 61 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B 61 " " NAG B1313 " - " ASN B 165 " " NAG B1314 " - " ASN B 331 " " NAG B1315 " - " ASN B 343 " " NAG B1316 " - " ASN B1074 " " 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 282 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C 801 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 165 " " NAG C1314 " - " ASN C 234 " " NAG C1315 " - " ASN C 343 " Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 64 sheets defined 22.9% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.571A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.414A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.988A 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 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.732A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.507A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.725A 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 886 through 891 removed outlier: 3.690A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.909A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 4.282A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 30 No H-bonds generated for 'chain 'X' and resid 28 through 30' Processing helix chain 'X' and resid 61 through 64 removed outlier: 3.834A pdb=" N LYS X 64 " --> pdb=" O ASP X 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 61 through 64' Processing helix chain 'X' and resid 83 through 87 Processing helix chain 'Y' and resid 79 through 83 removed outlier: 3.620A pdb=" N VAL Y 83 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.658A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.398A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.899A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.949A 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 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.656A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.559A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 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: 4.704A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.972A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.641A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100A through 100E Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.893A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (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 349 through 353 removed outlier: 3.556A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.155A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.059A 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 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.996A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.523A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.612A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.602A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.744A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.654A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.715A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.736A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.802A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.912A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100A through 100E Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.726A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.007A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.988A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.733A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.103A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.215A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.563A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.551A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.543A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.446A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'X' and resid 10 through 12 removed outlier: 5.370A pdb=" N ASP X 33 " --> pdb=" O ASP X 95 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 10 through 12 removed outlier: 7.136A pdb=" N CYS X 92 " --> pdb=" O TRP X 103 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TRP X 103 " --> pdb=" O CYS X 92 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG X 94 " --> pdb=" O ASP X 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'Y' and resid 10 through 12 removed outlier: 4.595A pdb=" N LEU Y 33 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR Y 49 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU Y 50 " --> pdb=" O ASN Y 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.166A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.958A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.778A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.387A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.323A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.178A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.275A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.531A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.955A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.900A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.316A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.237A pdb=" N ILE A 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 'A' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.185A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.745A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.867A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.867A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.896A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.010A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.849A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.314A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.175A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.045A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.161A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.866A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.957A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.195A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.437A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.585A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.101A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.635A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.829A pdb=" N ALA N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 75 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.987A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 10 through 13 removed outlier: 4.289A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3267 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: 9.31 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5026 1.32 - 1.46: 9957 1.46 - 1.59: 15669 1.59 - 1.72: 0 1.72 - 1.85: 177 Bond restraints: 30829 Sorted by residual: bond pdb=" C LYS L 24 " pdb=" O LYS L 24 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.19e-02 7.06e+03 1.39e+01 bond pdb=" N LEU L 46 " pdb=" CA LEU L 46 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.22e-02 6.72e+03 1.15e+01 bond pdb=" N ILE B 358 " pdb=" CA ILE B 358 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" N ILE Y 92 " pdb=" CA ILE Y 92 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.07e+00 bond pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.07e+00 ... (remaining 30824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 40998 2.16 - 4.31: 775 4.31 - 6.47: 157 6.47 - 8.63: 8 8.63 - 10.78: 7 Bond angle restraints: 41945 Sorted by residual: angle pdb=" CA MET M 82 " pdb=" C MET M 82 " pdb=" O MET M 82 " ideal model delta sigma weight residual 121.46 115.20 6.26 1.17e+00 7.31e-01 2.86e+01 angle pdb=" CA GLY B 744 " pdb=" C GLY B 744 " pdb=" O GLY B 744 " ideal model delta sigma weight residual 121.18 116.70 4.48 8.80e-01 1.29e+00 2.59e+01 angle pdb=" CA TYR C 160 " pdb=" C TYR C 160 " pdb=" O TYR C 160 " ideal model delta sigma weight residual 121.23 116.18 5.05 1.07e+00 8.73e-01 2.23e+01 angle pdb=" N LYS M 57 " pdb=" CA LYS M 57 " pdb=" C LYS M 57 " ideal model delta sigma weight residual 109.59 117.04 -7.45 1.61e+00 3.86e-01 2.14e+01 angle pdb=" CA LYS M 57 " pdb=" C LYS M 57 " pdb=" O LYS M 57 " ideal model delta sigma weight residual 120.71 115.83 4.88 1.06e+00 8.90e-01 2.12e+01 ... (remaining 41940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17534 17.96 - 35.92: 1133 35.92 - 53.89: 199 53.89 - 71.85: 51 71.85 - 89.81: 25 Dihedral angle restraints: 18942 sinusoidal: 7998 harmonic: 10944 Sorted by residual: 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 93.00 42.90 50.10 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -37.01 -48.99 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 45.14 47.86 1 1.00e+01 1.00e-02 3.16e+01 ... (remaining 18939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4428 0.088 - 0.176: 418 0.176 - 0.264: 11 0.264 - 0.352: 0 0.352 - 0.440: 1 Chirality restraints: 4858 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.84 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA PHE M 58 " pdb=" N PHE M 58 " pdb=" C PHE M 58 " pdb=" CB PHE M 58 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA CYS C 166 " pdb=" N CYS C 166 " pdb=" C CYS C 166 " pdb=" CB CYS C 166 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 4855 not shown) Planarity restraints: 5416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " -0.048 2.00e-02 2.50e+03 3.39e-02 2.88e+01 pdb=" CG TRP B 886 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 67 " 0.024 2.00e-02 2.50e+03 2.99e-02 1.57e+01 pdb=" CG PHE M 67 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE M 67 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE M 67 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE M 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE M 67 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE M 67 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 14 " -0.062 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO N 15 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO N 15 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO N 15 " -0.051 5.00e-02 4.00e+02 ... (remaining 5413 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4334 2.76 - 3.29: 29420 3.29 - 3.83: 48664 3.83 - 4.36: 60064 4.36 - 4.90: 105030 Nonbonded interactions: 247512 Sorted by model distance: nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU C 773 " pdb=" NE ARG C1019 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR A 108 " pdb=" O6 NAG A1305 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.260 3.040 ... (remaining 247507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 1315) selection = (chain 'B' and resid 27 through 1315) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Y' } 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: 7.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 31.500 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.005 0.101 30921 Z= 0.237 Angle : 0.779 14.303 42176 Z= 0.432 Chirality : 0.048 0.440 4858 Planarity : 0.005 0.119 5369 Dihedral : 12.649 89.809 11781 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3705 helix: 1.79 (0.21), residues: 645 sheet: -0.13 (0.16), residues: 1050 loop : -0.22 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG X 83 TYR 0.053 0.001 TYR C 904 PHE 0.068 0.001 PHE M 67 TRP 0.089 0.002 TRP B 886 HIS 0.012 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00465 (30829) covalent geometry : angle 0.75922 (41945) SS BOND : bond 0.00453 ( 45) SS BOND : angle 1.63733 ( 90) hydrogen bonds : bond 0.19018 ( 1205) hydrogen bonds : angle 8.15641 ( 3267) link_NAG-ASN : bond 0.01491 ( 47) link_NAG-ASN : angle 2.86206 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 68 THR cc_start: 0.9401 (m) cc_final: 0.9178 (p) REVERT: X 77 THR cc_start: 0.9064 (p) cc_final: 0.8797 (p) REVERT: X 82 MET cc_start: 0.8919 (mmm) cc_final: 0.8713 (mmt) REVERT: X 101 ASP cc_start: 0.8778 (t0) cc_final: 0.8439 (t0) REVERT: Y 2 ASN cc_start: 0.8285 (t0) cc_final: 0.8009 (t0) REVERT: Y 11 LEU cc_start: 0.8123 (tp) cc_final: 0.7498 (tp) REVERT: Y 30 LYS cc_start: 0.8995 (mttm) cc_final: 0.8793 (mttt) REVERT: Y 73 LEU cc_start: 0.8991 (tt) cc_final: 0.8301 (tt) REVERT: Y 75 ILE cc_start: 0.8043 (mp) cc_final: 0.7755 (tp) REVERT: Y 77 ARG cc_start: 0.7623 (ptm160) cc_final: 0.7310 (ptm160) REVERT: Y 79 GLU cc_start: 0.7863 (mp0) cc_final: 0.7537 (mp0) REVERT: Y 97 THR cc_start: 0.7927 (p) cc_final: 0.7272 (p) REVERT: Y 105 GLU cc_start: 0.7555 (pt0) cc_final: 0.7012 (pm20) REVERT: H 6 GLU cc_start: 0.7696 (mp0) cc_final: 0.7472 (mp0) REVERT: H 23 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7404 (tm-30) REVERT: H 32 TYR cc_start: 0.9145 (m-80) cc_final: 0.8872 (m-80) REVERT: H 64 LYS cc_start: 0.9278 (tptt) cc_final: 0.8739 (mmmt) REVERT: H 100 ASP cc_start: 0.8637 (t0) cc_final: 0.8343 (t0) REVERT: L 45 GLN cc_start: 0.7007 (pm20) cc_final: 0.6480 (pm20) REVERT: L 61 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7443 (ptp90) REVERT: L 79 GLU cc_start: 0.7960 (mp0) cc_final: 0.7328 (mp0) REVERT: L 82 ASP cc_start: 0.8641 (m-30) cc_final: 0.8402 (m-30) REVERT: L 103 LYS cc_start: 0.8192 (tmtt) cc_final: 0.7992 (tptp) REVERT: L 104 LEU cc_start: 0.8329 (tt) cc_final: 0.8013 (tt) REVERT: M 72 ASP cc_start: 0.8878 (t0) cc_final: 0.8277 (t0) REVERT: N 11 LEU cc_start: 0.8599 (pt) cc_final: 0.8391 (pt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.2032 time to fit residues: 111.3560 Evaluate side-chains 277 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 394 ASN B1002 GLN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN C 121 ASN M 82AASN N 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.087772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056623 restraints weight = 77854.859| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.98 r_work: 0.2817 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30921 Z= 0.144 Angle : 0.572 11.435 42176 Z= 0.291 Chirality : 0.045 0.225 4858 Planarity : 0.004 0.064 5369 Dihedral : 5.669 55.226 5046 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 4.31 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3705 helix: 2.25 (0.21), residues: 606 sheet: 0.06 (0.16), residues: 1044 loop : -0.22 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1107 TYR 0.023 0.001 TYR B1067 PHE 0.021 0.001 PHE N 55 TRP 0.033 0.001 TRP Y 35 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00329 (30829) covalent geometry : angle 0.55982 (41945) SS BOND : bond 0.00453 ( 45) SS BOND : angle 1.30007 ( 90) hydrogen bonds : bond 0.04261 ( 1205) hydrogen bonds : angle 5.91412 ( 3267) link_NAG-ASN : bond 0.00157 ( 47) link_NAG-ASN : angle 1.90952 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 333 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8319 (pmm) cc_final: 0.8069 (pmm) REVERT: B 346 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7687 (ttp80) REVERT: B 402 ILE cc_start: 0.8737 (tt) cc_final: 0.8460 (tp) REVERT: B 904 TYR cc_start: 0.8405 (t80) cc_final: 0.8138 (t80) REVERT: B 941 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8566 (p) REVERT: X 16 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8424 (mtm-85) REVERT: X 23 GLU cc_start: 0.8899 (tp30) cc_final: 0.8682 (tp30) REVERT: X 64 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8400 (mmmt) REVERT: X 75 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8947 (ptpp) REVERT: X 77 THR cc_start: 0.8544 (p) cc_final: 0.7708 (p) REVERT: X 79 TYR cc_start: 0.8642 (m-80) cc_final: 0.8055 (m-10) REVERT: X 82 MET cc_start: 0.8969 (mmm) cc_final: 0.8694 (mmt) REVERT: X 101 ASP cc_start: 0.9010 (t0) cc_final: 0.8749 (t0) REVERT: Y 2 ASN cc_start: 0.8050 (t0) cc_final: 0.7562 (t0) REVERT: Y 11 LEU cc_start: 0.8055 (tp) cc_final: 0.7385 (tp) REVERT: Y 34 TYR cc_start: 0.8738 (m-80) cc_final: 0.8444 (m-80) REVERT: Y 54 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7725 (ptp90) REVERT: Y 61 ARG cc_start: 0.8444 (ptt-90) cc_final: 0.8205 (ptt-90) REVERT: Y 81 GLU cc_start: 0.8893 (pm20) cc_final: 0.8511 (pm20) REVERT: Y 105 GLU cc_start: 0.7267 (pt0) cc_final: 0.6786 (pm20) REVERT: H 23 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7835 (tm-30) REVERT: H 32 TYR cc_start: 0.9083 (m-80) cc_final: 0.8790 (m-80) REVERT: H 46 GLU cc_start: 0.8387 (tt0) cc_final: 0.8081 (pt0) REVERT: H 64 LYS cc_start: 0.9330 (tptt) cc_final: 0.8630 (mmmt) REVERT: H 72 ASP cc_start: 0.8583 (t0) cc_final: 0.8372 (t0) REVERT: H 82 MET cc_start: 0.8237 (mtt) cc_final: 0.7955 (mtt) REVERT: H 105 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8145 (mm-40) REVERT: L 24 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8831 (mmmt) REVERT: L 61 ARG cc_start: 0.8331 (ptp90) cc_final: 0.8068 (ptp90) REVERT: L 79 GLU cc_start: 0.7922 (mp0) cc_final: 0.7604 (mp0) REVERT: L 82 ASP cc_start: 0.8389 (m-30) cc_final: 0.7525 (m-30) REVERT: L 104 LEU cc_start: 0.8170 (tt) cc_final: 0.7491 (tt) REVERT: C 140 PHE cc_start: 0.8204 (p90) cc_final: 0.7907 (p90) REVERT: C 568 ASP cc_start: 0.8555 (t0) cc_final: 0.8329 (m-30) REVERT: C 904 TYR cc_start: 0.8293 (m-80) cc_final: 0.7934 (m-80) REVERT: M 13 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8647 (mm-40) REVERT: M 32 TYR cc_start: 0.8897 (m-80) cc_final: 0.8642 (m-80) REVERT: M 46 GLU cc_start: 0.8680 (tt0) cc_final: 0.8405 (tt0) REVERT: M 72 ASP cc_start: 0.8932 (t0) cc_final: 0.8539 (t0) REVERT: M 100 ASP cc_start: 0.8853 (t0) cc_final: 0.8601 (t0) REVERT: N 4 MET cc_start: 0.8433 (tpt) cc_final: 0.8114 (mmm) REVERT: N 24 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8750 (mmmt) REVERT: N 54 ARG cc_start: 0.8000 (ptp90) cc_final: 0.7689 (ptp90) REVERT: N 55 PHE cc_start: 0.8996 (t80) cc_final: 0.8680 (t80) REVERT: N 61 ARG cc_start: 0.8406 (ptt-90) cc_final: 0.8024 (ptt-90) REVERT: N 77 ARG cc_start: 0.8421 (ptm160) cc_final: 0.8144 (mtp-110) REVERT: N 79 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7440 (mm-30) outliers start: 28 outliers final: 19 residues processed: 344 average time/residue: 0.2020 time to fit residues: 109.7460 Evaluate side-chains 307 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 287 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 133 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 205 optimal weight: 0.0470 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 39 GLN Y 38 GLN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054025 restraints weight = 78116.924| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.97 r_work: 0.2754 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30921 Z= 0.245 Angle : 0.603 11.688 42176 Z= 0.304 Chirality : 0.046 0.239 4858 Planarity : 0.004 0.053 5369 Dihedral : 5.543 54.561 5046 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.46 % Allowed : 6.56 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3705 helix: 1.76 (0.21), residues: 654 sheet: 0.05 (0.15), residues: 1053 loop : -0.27 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.030 0.001 TYR Y 49 PHE 0.019 0.002 PHE N 96 TRP 0.035 0.001 TRP Y 35 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00577 (30829) covalent geometry : angle 0.58996 (41945) SS BOND : bond 0.00459 ( 45) SS BOND : angle 1.45984 ( 90) hydrogen bonds : bond 0.04293 ( 1205) hydrogen bonds : angle 5.70525 ( 3267) link_NAG-ASN : bond 0.00199 ( 47) link_NAG-ASN : angle 1.95512 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8302 (pmm) cc_final: 0.7937 (pmm) REVERT: B 394 ASN cc_start: 0.7970 (t0) cc_final: 0.7624 (t0) REVERT: B 402 ILE cc_start: 0.8692 (tt) cc_final: 0.8389 (tp) REVERT: X 16 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8401 (mtm-85) REVERT: X 64 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8371 (mmmm) REVERT: X 77 THR cc_start: 0.8540 (p) cc_final: 0.7558 (p) REVERT: X 79 TYR cc_start: 0.8542 (m-80) cc_final: 0.8006 (m-10) REVERT: X 82 MET cc_start: 0.8779 (mmm) cc_final: 0.8524 (mmt) REVERT: X 82 LEU cc_start: 0.8638 (mt) cc_final: 0.8381 (mt) REVERT: X 100 ASP cc_start: 0.8999 (t0) cc_final: 0.8763 (t0) REVERT: X 101 ASP cc_start: 0.9047 (t0) cc_final: 0.8813 (t0) REVERT: Y 2 ASN cc_start: 0.8040 (t0) cc_final: 0.7669 (t0) REVERT: Y 11 LEU cc_start: 0.8119 (tp) cc_final: 0.7389 (tp) REVERT: Y 61 ARG cc_start: 0.8486 (ptt-90) cc_final: 0.8270 (ptt-90) REVERT: Y 93 GLN cc_start: 0.8918 (tp40) cc_final: 0.8671 (tp40) REVERT: Y 103 LYS cc_start: 0.9069 (tptp) cc_final: 0.8787 (tptp) REVERT: Y 105 GLU cc_start: 0.7162 (pt0) cc_final: 0.6742 (pm20) REVERT: A 904 TYR cc_start: 0.8690 (t80) cc_final: 0.8239 (t80) REVERT: H 23 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7865 (tm-30) REVERT: H 46 GLU cc_start: 0.8351 (tt0) cc_final: 0.7881 (tt0) REVERT: H 72 ASP cc_start: 0.8691 (t0) cc_final: 0.8393 (t0) REVERT: H 105 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8111 (mm-40) REVERT: L 24 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8957 (mmmt) REVERT: L 54 ARG cc_start: 0.8599 (ptp90) cc_final: 0.8348 (ptp90) REVERT: L 60 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8013 (mm-30) REVERT: L 61 ARG cc_start: 0.8206 (ptp90) cc_final: 0.7964 (ptp90) REVERT: L 79 GLU cc_start: 0.7843 (mp0) cc_final: 0.7472 (mp0) REVERT: L 82 ASP cc_start: 0.8156 (m-30) cc_final: 0.7546 (m-30) REVERT: L 104 LEU cc_start: 0.7618 (tt) cc_final: 0.7369 (tt) REVERT: C 455 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7849 (mt) REVERT: C 568 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: C 904 TYR cc_start: 0.8463 (m-80) cc_final: 0.8175 (m-10) REVERT: M 13 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8664 (mm110) REVERT: M 46 GLU cc_start: 0.8710 (tt0) cc_final: 0.8410 (tt0) REVERT: M 59 TYR cc_start: 0.8127 (m-80) cc_final: 0.7892 (m-80) REVERT: M 64 LYS cc_start: 0.9071 (tppt) cc_final: 0.8862 (tppt) REVERT: M 72 ASP cc_start: 0.8949 (t0) cc_final: 0.8527 (t0) REVERT: M 79 TYR cc_start: 0.9106 (m-10) cc_final: 0.8848 (m-10) REVERT: M 100 ASP cc_start: 0.8886 (t0) cc_final: 0.8561 (t0) REVERT: N 4 MET cc_start: 0.8108 (tpt) cc_final: 0.7635 (mmm) REVERT: N 55 PHE cc_start: 0.9068 (t80) cc_final: 0.8629 (t80) REVERT: N 61 ARG cc_start: 0.8719 (ptt-90) cc_final: 0.8472 (ptt-90) outliers start: 48 outliers final: 27 residues processed: 328 average time/residue: 0.1981 time to fit residues: 103.1207 Evaluate side-chains 316 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 9 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 347 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN N 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.086820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.055789 restraints weight = 77198.197| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.97 r_work: 0.2804 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30921 Z= 0.132 Angle : 0.539 11.202 42176 Z= 0.271 Chirality : 0.044 0.236 4858 Planarity : 0.003 0.050 5369 Dihedral : 5.260 53.753 5046 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.70 % Allowed : 7.44 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3705 helix: 2.03 (0.21), residues: 642 sheet: 0.18 (0.15), residues: 1011 loop : -0.27 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 83 TYR 0.027 0.001 TYR Y 49 PHE 0.016 0.001 PHE N 71 TRP 0.019 0.001 TRP Y 35 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00304 (30829) covalent geometry : angle 0.52700 (41945) SS BOND : bond 0.00327 ( 45) SS BOND : angle 1.28213 ( 90) hydrogen bonds : bond 0.03682 ( 1205) hydrogen bonds : angle 5.42077 ( 3267) link_NAG-ASN : bond 0.00130 ( 47) link_NAG-ASN : angle 1.78971 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8271 (pmm) cc_final: 0.7926 (pmm) REVERT: B 394 ASN cc_start: 0.7847 (t0) cc_final: 0.7420 (t0) REVERT: B 402 ILE cc_start: 0.8686 (tt) cc_final: 0.8373 (tp) REVERT: X 46 GLU cc_start: 0.8814 (tp30) cc_final: 0.8199 (tt0) REVERT: X 64 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8493 (mmmm) REVERT: X 77 THR cc_start: 0.8355 (p) cc_final: 0.7080 (p) REVERT: X 79 TYR cc_start: 0.8666 (m-80) cc_final: 0.8022 (m-10) REVERT: X 82 MET cc_start: 0.8740 (mmm) cc_final: 0.8523 (mmt) REVERT: X 82 LEU cc_start: 0.8756 (mt) cc_final: 0.8549 (mt) REVERT: X 86 ASP cc_start: 0.8052 (m-30) cc_final: 0.7812 (m-30) REVERT: X 100 ASP cc_start: 0.9013 (t0) cc_final: 0.8744 (t0) REVERT: X 101 ASP cc_start: 0.9035 (t0) cc_final: 0.8833 (t0) REVERT: Y 11 LEU cc_start: 0.8106 (tp) cc_final: 0.7510 (tp) REVERT: Y 34 TYR cc_start: 0.8800 (m-80) cc_final: 0.8217 (m-80) REVERT: Y 45 GLN cc_start: 0.8802 (tt0) cc_final: 0.8376 (pt0) REVERT: Y 61 ARG cc_start: 0.8482 (ptt-90) cc_final: 0.8274 (ptt-90) REVERT: Y 89 MET cc_start: 0.9152 (ttp) cc_final: 0.8195 (ttp) REVERT: Y 93 GLN cc_start: 0.8939 (tp40) cc_final: 0.8709 (tp40) REVERT: Y 100 GLN cc_start: 0.8590 (pm20) cc_final: 0.8275 (pm20) REVERT: Y 103 LYS cc_start: 0.9061 (tptp) cc_final: 0.8645 (tptp) REVERT: Y 105 GLU cc_start: 0.7079 (pt0) cc_final: 0.6622 (pm20) REVERT: A 586 ASP cc_start: 0.8728 (m-30) cc_final: 0.8417 (m-30) REVERT: H 23 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7867 (tm-30) REVERT: H 46 GLU cc_start: 0.8380 (tt0) cc_final: 0.7913 (tt0) REVERT: H 72 ASP cc_start: 0.8767 (t0) cc_final: 0.8430 (t0) REVERT: H 82 MET cc_start: 0.8221 (mtt) cc_final: 0.7953 (mtt) REVERT: H 105 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8178 (mm-40) REVERT: L 31 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8313 (t) REVERT: L 54 ARG cc_start: 0.8624 (ptp90) cc_final: 0.8340 (ptp90) REVERT: L 60 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7957 (mm-30) REVERT: L 61 ARG cc_start: 0.8305 (ptp90) cc_final: 0.8069 (ptp90) REVERT: L 79 GLU cc_start: 0.7892 (mp0) cc_final: 0.7527 (mp0) REVERT: L 82 ASP cc_start: 0.8091 (m-30) cc_final: 0.7426 (m-30) REVERT: L 103 LYS cc_start: 0.8109 (tptp) cc_final: 0.7877 (tptp) REVERT: C 455 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7886 (mt) REVERT: C 904 TYR cc_start: 0.8268 (m-80) cc_final: 0.8038 (m-10) REVERT: C 1096 VAL cc_start: 0.9551 (OUTLIER) cc_final: 0.9294 (m) REVERT: M 13 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8326 (mm110) REVERT: M 46 GLU cc_start: 0.8745 (tt0) cc_final: 0.8431 (tt0) REVERT: M 59 TYR cc_start: 0.8109 (m-80) cc_final: 0.7768 (m-80) REVERT: M 64 LYS cc_start: 0.9054 (tppt) cc_final: 0.8825 (tppt) REVERT: M 72 ASP cc_start: 0.8951 (t0) cc_final: 0.8304 (t0) REVERT: M 75 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8889 (ptpp) REVERT: M 79 TYR cc_start: 0.9162 (m-10) cc_final: 0.8896 (m-10) REVERT: M 100 ASP cc_start: 0.8886 (t0) cc_final: 0.8522 (t0) REVERT: N 4 MET cc_start: 0.8016 (tpt) cc_final: 0.7554 (mmm) REVERT: N 37 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8546 (pt) REVERT: N 55 PHE cc_start: 0.8940 (t80) cc_final: 0.8523 (t80) REVERT: N 61 ARG cc_start: 0.8740 (ptt-90) cc_final: 0.8417 (ptt-90) REVERT: N 93 GLN cc_start: 0.8388 (tp40) cc_final: 0.7935 (tp-100) outliers start: 56 outliers final: 32 residues processed: 336 average time/residue: 0.1941 time to fit residues: 104.3464 Evaluate side-chains 323 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 60 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 353 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 chunk 349 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B1088 HIS ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN H 56 ASN L 6 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS N 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.084934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053774 restraints weight = 78276.021| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.97 r_work: 0.2745 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 30921 Z= 0.268 Angle : 0.609 11.315 42176 Z= 0.306 Chirality : 0.046 0.248 4858 Planarity : 0.004 0.047 5369 Dihedral : 5.456 54.576 5046 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.88 % Allowed : 8.38 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3705 helix: 1.75 (0.21), residues: 651 sheet: 0.13 (0.16), residues: 1005 loop : -0.35 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 16 TYR 0.027 0.001 TYR N 49 PHE 0.020 0.001 PHE M 67 TRP 0.025 0.001 TRP B 886 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00633 (30829) covalent geometry : angle 0.59543 (41945) SS BOND : bond 0.00503 ( 45) SS BOND : angle 1.65477 ( 90) hydrogen bonds : bond 0.04122 ( 1205) hydrogen bonds : angle 5.51046 ( 3267) link_NAG-ASN : bond 0.00236 ( 47) link_NAG-ASN : angle 1.93610 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8248 (pmm) cc_final: 0.7901 (pmm) REVERT: B 394 ASN cc_start: 0.8030 (t0) cc_final: 0.7523 (t0) REVERT: B 402 ILE cc_start: 0.8715 (tt) cc_final: 0.8425 (tp) REVERT: X 64 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8560 (mmmm) REVERT: X 77 THR cc_start: 0.8535 (p) cc_final: 0.7574 (p) REVERT: X 79 TYR cc_start: 0.8699 (m-80) cc_final: 0.8094 (m-10) REVERT: X 82 MET cc_start: 0.8687 (mmm) cc_final: 0.8476 (mmt) REVERT: X 86 ASP cc_start: 0.8056 (m-30) cc_final: 0.7836 (m-30) REVERT: X 100 ASP cc_start: 0.9032 (t0) cc_final: 0.8752 (t0) REVERT: X 101 ASP cc_start: 0.9056 (t0) cc_final: 0.8839 (t0) REVERT: Y 11 LEU cc_start: 0.8113 (tp) cc_final: 0.7568 (tp) REVERT: Y 61 ARG cc_start: 0.8461 (ptt-90) cc_final: 0.8246 (ptt-90) REVERT: Y 77 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7786 (mtp85) REVERT: Y 93 GLN cc_start: 0.8927 (tp40) cc_final: 0.8686 (tp40) REVERT: Y 100 GLN cc_start: 0.8646 (pm20) cc_final: 0.8325 (pm20) REVERT: Y 105 GLU cc_start: 0.6981 (pt0) cc_final: 0.6534 (pm20) REVERT: H 23 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7889 (tm-30) REVERT: H 46 GLU cc_start: 0.8381 (tt0) cc_final: 0.7928 (tt0) REVERT: H 72 ASP cc_start: 0.8853 (t0) cc_final: 0.8468 (t0) REVERT: H 105 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8112 (mm-40) REVERT: L 31 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8291 (t) REVERT: L 54 ARG cc_start: 0.8647 (ptp90) cc_final: 0.8401 (ptp90) REVERT: L 60 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8051 (mm-30) REVERT: L 61 ARG cc_start: 0.8210 (ptp90) cc_final: 0.8004 (ptp90) REVERT: L 79 GLU cc_start: 0.7828 (mp0) cc_final: 0.7554 (mp0) REVERT: L 82 ASP cc_start: 0.8165 (m-30) cc_final: 0.7509 (m-30) REVERT: C 455 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7885 (mt) REVERT: C 904 TYR cc_start: 0.8520 (m-80) cc_final: 0.8276 (m-10) REVERT: M 13 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8314 (mm110) REVERT: M 46 GLU cc_start: 0.8746 (tt0) cc_final: 0.8403 (tt0) REVERT: M 72 ASP cc_start: 0.8984 (t0) cc_final: 0.8540 (t0) REVERT: M 79 TYR cc_start: 0.9155 (m-10) cc_final: 0.8948 (m-10) REVERT: M 100 ASP cc_start: 0.8910 (t0) cc_final: 0.8515 (t0) REVERT: N 4 MET cc_start: 0.7976 (tpt) cc_final: 0.7477 (mmm) REVERT: N 37 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8576 (pt) REVERT: N 55 PHE cc_start: 0.9046 (t80) cc_final: 0.8530 (t80) REVERT: N 61 ARG cc_start: 0.8738 (ptt-90) cc_final: 0.8435 (ptt-90) outliers start: 62 outliers final: 46 residues processed: 333 average time/residue: 0.1895 time to fit residues: 101.1958 Evaluate side-chains 329 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 372 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 271 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 240 optimal weight: 0.0170 chunk 197 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 222 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN H 56 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.086461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.055477 restraints weight = 77654.860| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.98 r_work: 0.2800 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30921 Z= 0.115 Angle : 0.533 11.182 42176 Z= 0.267 Chirality : 0.043 0.227 4858 Planarity : 0.003 0.046 5369 Dihedral : 5.179 53.561 5046 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.79 % Allowed : 9.11 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3705 helix: 2.09 (0.21), residues: 642 sheet: 0.28 (0.16), residues: 975 loop : -0.29 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 16 TYR 0.027 0.001 TYR N 49 PHE 0.016 0.001 PHE M 67 TRP 0.014 0.001 TRP Y 35 HIS 0.004 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00259 (30829) covalent geometry : angle 0.52182 (41945) SS BOND : bond 0.00312 ( 45) SS BOND : angle 1.26473 ( 90) hydrogen bonds : bond 0.03523 ( 1205) hydrogen bonds : angle 5.25290 ( 3267) link_NAG-ASN : bond 0.00132 ( 47) link_NAG-ASN : angle 1.71228 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8264 (pmm) cc_final: 0.7883 (pmm) REVERT: B 394 ASN cc_start: 0.7873 (t0) cc_final: 0.7364 (t0) REVERT: B 402 ILE cc_start: 0.8691 (tt) cc_final: 0.8377 (tp) REVERT: B 531 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9090 (p) REVERT: X 46 GLU cc_start: 0.8815 (tp30) cc_final: 0.8142 (tt0) REVERT: X 64 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8603 (mmmm) REVERT: X 77 THR cc_start: 0.8488 (p) cc_final: 0.7460 (p) REVERT: X 79 TYR cc_start: 0.8764 (m-80) cc_final: 0.8156 (m-10) REVERT: X 82 MET cc_start: 0.8542 (mmm) cc_final: 0.8297 (mmt) REVERT: X 100 ASP cc_start: 0.9030 (t0) cc_final: 0.8764 (t0) REVERT: Y 11 LEU cc_start: 0.8123 (tp) cc_final: 0.7570 (tp) REVERT: Y 100 GLN cc_start: 0.8806 (pm20) cc_final: 0.8462 (pm20) REVERT: Y 103 LYS cc_start: 0.9081 (tptp) cc_final: 0.8683 (tptp) REVERT: Y 105 GLU cc_start: 0.6987 (pt0) cc_final: 0.6519 (pm20) REVERT: A 52 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 586 ASP cc_start: 0.8726 (m-30) cc_final: 0.8414 (m-30) REVERT: H 23 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7870 (tm-30) REVERT: H 46 GLU cc_start: 0.8388 (tt0) cc_final: 0.7910 (tt0) REVERT: H 72 ASP cc_start: 0.8881 (t0) cc_final: 0.8486 (t0) REVERT: H 105 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8141 (mm-40) REVERT: L 31 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8332 (t) REVERT: L 54 ARG cc_start: 0.8658 (ptp90) cc_final: 0.8381 (ptp90) REVERT: L 60 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8025 (mm-30) REVERT: L 61 ARG cc_start: 0.8257 (ptp90) cc_final: 0.7988 (ptp90) REVERT: L 79 GLU cc_start: 0.7939 (mp0) cc_final: 0.7535 (mp0) REVERT: L 82 ASP cc_start: 0.8225 (m-30) cc_final: 0.7357 (m-30) REVERT: L 100 GLN cc_start: 0.8551 (pm20) cc_final: 0.8295 (pm20) REVERT: C 455 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7806 (mt) REVERT: C 904 TYR cc_start: 0.8423 (m-80) cc_final: 0.8135 (m-10) REVERT: M 13 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8404 (mm110) REVERT: M 46 GLU cc_start: 0.8807 (tt0) cc_final: 0.8434 (tt0) REVERT: M 59 TYR cc_start: 0.8133 (m-80) cc_final: 0.7906 (m-80) REVERT: M 72 ASP cc_start: 0.8949 (t0) cc_final: 0.8279 (t0) REVERT: M 75 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8948 (ptpp) REVERT: M 100 ASP cc_start: 0.8914 (t0) cc_final: 0.8531 (t0) REVERT: N 4 MET cc_start: 0.7890 (tpt) cc_final: 0.7464 (mmm) REVERT: N 37 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8545 (pt) REVERT: N 54 ARG cc_start: 0.8162 (ptp90) cc_final: 0.7910 (ptp90) REVERT: N 61 ARG cc_start: 0.8733 (ptt-90) cc_final: 0.8408 (ptt-90) REVERT: N 79 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7471 (mm-30) REVERT: N 93 GLN cc_start: 0.8423 (tp40) cc_final: 0.7964 (tp-100) REVERT: N 98 PHE cc_start: 0.8069 (m-80) cc_final: 0.7766 (m-80) outliers start: 59 outliers final: 47 residues processed: 338 average time/residue: 0.2005 time to fit residues: 107.5628 Evaluate side-chains 336 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 284 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 56 optimal weight: 0.9980 chunk 262 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.085839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054727 restraints weight = 77673.836| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.98 r_work: 0.2767 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30921 Z= 0.160 Angle : 0.549 11.360 42176 Z= 0.274 Chirality : 0.044 0.228 4858 Planarity : 0.003 0.045 5369 Dihedral : 5.138 53.920 5046 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.79 % Allowed : 9.53 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3705 helix: 2.10 (0.21), residues: 642 sheet: 0.21 (0.16), residues: 1011 loop : -0.29 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 16 TYR 0.025 0.001 TYR N 49 PHE 0.018 0.001 PHE M 67 TRP 0.013 0.001 TRP Y 35 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00377 (30829) covalent geometry : angle 0.53791 (41945) SS BOND : bond 0.00360 ( 45) SS BOND : angle 1.30696 ( 90) hydrogen bonds : bond 0.03617 ( 1205) hydrogen bonds : angle 5.23582 ( 3267) link_NAG-ASN : bond 0.00129 ( 47) link_NAG-ASN : angle 1.69592 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 290 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8289 (pmm) cc_final: 0.7925 (pmm) REVERT: B 394 ASN cc_start: 0.7850 (t0) cc_final: 0.7327 (t0) REVERT: B 402 ILE cc_start: 0.8701 (tt) cc_final: 0.8407 (tp) REVERT: B 531 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9096 (p) REVERT: X 64 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8615 (mmmm) REVERT: X 77 THR cc_start: 0.8499 (p) cc_final: 0.7474 (p) REVERT: X 79 TYR cc_start: 0.8789 (m-80) cc_final: 0.8219 (m-10) REVERT: X 82 MET cc_start: 0.8529 (mmm) cc_final: 0.8278 (mmt) REVERT: X 100 ASP cc_start: 0.9056 (t0) cc_final: 0.8794 (t0) REVERT: Y 11 LEU cc_start: 0.8123 (tp) cc_final: 0.7570 (tp) REVERT: Y 45 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (pt0) REVERT: Y 61 ARG cc_start: 0.8271 (ptt-90) cc_final: 0.7899 (ptt-90) REVERT: Y 93 GLN cc_start: 0.8907 (tp40) cc_final: 0.8590 (tp-100) REVERT: Y 100 GLN cc_start: 0.8834 (pm20) cc_final: 0.8471 (pm20) REVERT: Y 103 LYS cc_start: 0.9070 (tptp) cc_final: 0.8685 (tptp) REVERT: Y 105 GLU cc_start: 0.6854 (pt0) cc_final: 0.6409 (pm20) REVERT: A 52 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8800 (tm-30) REVERT: A 586 ASP cc_start: 0.8738 (m-30) cc_final: 0.8433 (m-30) REVERT: H 13 GLN cc_start: 0.8924 (mp10) cc_final: 0.8510 (mp10) REVERT: H 19 ARG cc_start: 0.8790 (ttt-90) cc_final: 0.8490 (ttt-90) REVERT: H 23 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7882 (tm-30) REVERT: H 46 GLU cc_start: 0.8408 (tt0) cc_final: 0.7966 (tt0) REVERT: H 72 ASP cc_start: 0.8896 (t0) cc_final: 0.8440 (t0) REVERT: H 105 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8066 (mm-40) REVERT: L 31 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8326 (t) REVERT: L 54 ARG cc_start: 0.8663 (ptp90) cc_final: 0.8222 (ptp-110) REVERT: L 82 ASP cc_start: 0.8207 (m-30) cc_final: 0.7600 (m-30) REVERT: L 93 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8715 (pm20) REVERT: L 100 GLN cc_start: 0.8546 (pm20) cc_final: 0.8295 (pm20) REVERT: C 455 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7844 (mt) REVERT: C 519 HIS cc_start: 0.6901 (t-90) cc_final: 0.6556 (t-90) REVERT: C 904 TYR cc_start: 0.8487 (m-80) cc_final: 0.8186 (m-10) REVERT: M 13 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8443 (mm110) REVERT: M 46 GLU cc_start: 0.8815 (tt0) cc_final: 0.8450 (tt0) REVERT: M 59 TYR cc_start: 0.8070 (m-80) cc_final: 0.7377 (m-80) REVERT: M 64 LYS cc_start: 0.9099 (tppt) cc_final: 0.8619 (tppt) REVERT: M 72 ASP cc_start: 0.8974 (t0) cc_final: 0.8300 (t0) REVERT: M 75 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8920 (ptpp) REVERT: M 100 ASP cc_start: 0.8916 (t0) cc_final: 0.8537 (t0) REVERT: N 4 MET cc_start: 0.7849 (tpt) cc_final: 0.7489 (mmm) REVERT: N 37 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8509 (pt) REVERT: N 54 ARG cc_start: 0.8066 (ptp90) cc_final: 0.7791 (ptp90) REVERT: N 55 PHE cc_start: 0.8728 (t80) cc_final: 0.8511 (t80) REVERT: N 61 ARG cc_start: 0.8753 (ptt-90) cc_final: 0.8411 (ptt-90) REVERT: N 93 GLN cc_start: 0.8439 (tp40) cc_final: 0.7986 (tp-100) REVERT: N 98 PHE cc_start: 0.8079 (m-80) cc_final: 0.7799 (m-80) outliers start: 59 outliers final: 44 residues processed: 326 average time/residue: 0.1934 time to fit residues: 101.1222 Evaluate side-chains 333 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 156 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 366 optimal weight: 20.0000 chunk 291 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 159 optimal weight: 0.0970 chunk 231 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.087883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056998 restraints weight = 78387.507| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.09 r_work: 0.2841 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30921 Z= 0.103 Angle : 0.524 11.228 42176 Z= 0.260 Chirality : 0.043 0.215 4858 Planarity : 0.003 0.045 5369 Dihedral : 4.945 53.731 5046 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.88 % Allowed : 9.84 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3705 helix: 2.41 (0.21), residues: 624 sheet: 0.33 (0.16), residues: 993 loop : -0.21 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 19 TYR 0.029 0.001 TYR A 489 PHE 0.011 0.001 PHE N 71 TRP 0.013 0.001 TRP Y 35 HIS 0.004 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00230 (30829) covalent geometry : angle 0.51531 (41945) SS BOND : bond 0.00293 ( 45) SS BOND : angle 1.02380 ( 90) hydrogen bonds : bond 0.03299 ( 1205) hydrogen bonds : angle 5.04365 ( 3267) link_NAG-ASN : bond 0.00134 ( 47) link_NAG-ASN : angle 1.55917 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8234 (pmm) cc_final: 0.7865 (pmm) REVERT: B 394 ASN cc_start: 0.7700 (t0) cc_final: 0.7163 (t0) REVERT: B 402 ILE cc_start: 0.8651 (tt) cc_final: 0.8355 (tp) REVERT: B 531 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9090 (p) REVERT: X 46 GLU cc_start: 0.8693 (tp30) cc_final: 0.7986 (tt0) REVERT: X 64 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8625 (mmmm) REVERT: X 77 THR cc_start: 0.8277 (p) cc_final: 0.7203 (p) REVERT: X 79 TYR cc_start: 0.8695 (m-80) cc_final: 0.8168 (m-10) REVERT: X 100 ASP cc_start: 0.8942 (t0) cc_final: 0.8647 (t0) REVERT: Y 11 LEU cc_start: 0.8087 (tp) cc_final: 0.7533 (tp) REVERT: Y 45 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8418 (pt0) REVERT: Y 61 ARG cc_start: 0.8185 (ptt-90) cc_final: 0.7848 (ptt-90) REVERT: Y 100 GLN cc_start: 0.8856 (pm20) cc_final: 0.8453 (pm20) REVERT: Y 103 LYS cc_start: 0.9069 (tptp) cc_final: 0.8695 (tptp) REVERT: Y 105 GLU cc_start: 0.6774 (pt0) cc_final: 0.6361 (pm20) REVERT: A 52 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 586 ASP cc_start: 0.8462 (m-30) cc_final: 0.8164 (m-30) REVERT: H 23 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7761 (tm-30) REVERT: H 46 GLU cc_start: 0.8371 (tt0) cc_final: 0.7903 (tt0) REVERT: H 72 ASP cc_start: 0.8738 (t0) cc_final: 0.8317 (t0) REVERT: H 100 MET cc_start: 0.8753 (mpp) cc_final: 0.8405 (mpp) REVERT: H 105 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7968 (mm110) REVERT: L 31 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8236 (t) REVERT: L 79 GLU cc_start: 0.8025 (mp0) cc_final: 0.7751 (mp0) REVERT: L 82 ASP cc_start: 0.8158 (m-30) cc_final: 0.7647 (m-30) REVERT: L 93 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8713 (pm20) REVERT: C 455 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7772 (mt) REVERT: C 519 HIS cc_start: 0.6842 (t-90) cc_final: 0.6435 (t-90) REVERT: C 904 TYR cc_start: 0.8095 (m-80) cc_final: 0.7763 (m-10) REVERT: M 13 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8451 (mm110) REVERT: M 46 GLU cc_start: 0.8823 (tt0) cc_final: 0.8532 (tt0) REVERT: M 59 TYR cc_start: 0.7903 (m-80) cc_final: 0.7550 (m-80) REVERT: M 67 PHE cc_start: 0.7549 (m-10) cc_final: 0.7023 (m-10) REVERT: M 72 ASP cc_start: 0.8769 (t0) cc_final: 0.8007 (t0) REVERT: M 75 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8848 (ptpp) REVERT: M 100 ASP cc_start: 0.8719 (t0) cc_final: 0.8306 (t0) REVERT: N 4 MET cc_start: 0.7834 (tpt) cc_final: 0.7471 (mmm) REVERT: N 37 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8460 (pt) REVERT: N 42 GLN cc_start: 0.8223 (pt0) cc_final: 0.7383 (pm20) REVERT: N 54 ARG cc_start: 0.8031 (ptp90) cc_final: 0.7768 (ptp90) REVERT: N 61 ARG cc_start: 0.8710 (ptt-90) cc_final: 0.8360 (ptt-90) REVERT: N 98 PHE cc_start: 0.7968 (m-80) cc_final: 0.7323 (m-80) outliers start: 62 outliers final: 47 residues processed: 339 average time/residue: 0.1907 time to fit residues: 103.9400 Evaluate side-chains 340 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 2 ASN Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 59 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 210 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.087753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056747 restraints weight = 78576.186| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.11 r_work: 0.2832 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30921 Z= 0.116 Angle : 0.531 11.201 42176 Z= 0.264 Chirality : 0.043 0.212 4858 Planarity : 0.003 0.046 5369 Dihedral : 4.903 53.704 5046 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.85 % Allowed : 10.20 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3705 helix: 2.44 (0.21), residues: 624 sheet: 0.35 (0.16), residues: 1011 loop : -0.20 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 83 TYR 0.027 0.001 TYR A 489 PHE 0.014 0.001 PHE N 55 TRP 0.017 0.001 TRP Y 35 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00269 (30829) covalent geometry : angle 0.52222 (41945) SS BOND : bond 0.00304 ( 45) SS BOND : angle 1.11852 ( 90) hydrogen bonds : bond 0.03354 ( 1205) hydrogen bonds : angle 5.01739 ( 3267) link_NAG-ASN : bond 0.00121 ( 47) link_NAG-ASN : angle 1.55410 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8276 (pmm) cc_final: 0.7915 (pmm) REVERT: B 394 ASN cc_start: 0.7714 (t0) cc_final: 0.7172 (t0) REVERT: B 402 ILE cc_start: 0.8669 (tt) cc_final: 0.8397 (tp) REVERT: B 531 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9105 (p) REVERT: X 46 GLU cc_start: 0.8689 (tp30) cc_final: 0.7997 (tt0) REVERT: X 64 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8607 (mmmm) REVERT: X 77 THR cc_start: 0.8283 (p) cc_final: 0.7140 (p) REVERT: X 79 TYR cc_start: 0.8752 (m-80) cc_final: 0.8065 (m-10) REVERT: X 82 MET cc_start: 0.8781 (mmt) cc_final: 0.8408 (mmt) REVERT: X 100 ASP cc_start: 0.8954 (t0) cc_final: 0.8663 (t0) REVERT: Y 11 LEU cc_start: 0.8128 (tp) cc_final: 0.7567 (tp) REVERT: Y 45 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8507 (pt0) REVERT: Y 79 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: Y 100 GLN cc_start: 0.8846 (pm20) cc_final: 0.8444 (pm20) REVERT: Y 103 LYS cc_start: 0.9070 (tptp) cc_final: 0.8690 (tptp) REVERT: Y 105 GLU cc_start: 0.6698 (pt0) cc_final: 0.6254 (pm20) REVERT: A 52 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8659 (tm-30) REVERT: A 586 ASP cc_start: 0.8473 (m-30) cc_final: 0.8186 (m-30) REVERT: H 23 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7756 (tm-30) REVERT: H 46 GLU cc_start: 0.8399 (tt0) cc_final: 0.7913 (tt0) REVERT: H 72 ASP cc_start: 0.8795 (t0) cc_final: 0.8377 (t0) REVERT: H 105 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7957 (mm110) REVERT: L 31 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8274 (t) REVERT: L 54 ARG cc_start: 0.8725 (ptp90) cc_final: 0.8512 (ptp90) REVERT: L 79 GLU cc_start: 0.8029 (mp0) cc_final: 0.7679 (mp0) REVERT: L 82 ASP cc_start: 0.8245 (m-30) cc_final: 0.7675 (m-30) REVERT: L 93 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8749 (pm20) REVERT: C 455 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7762 (mt) REVERT: C 519 HIS cc_start: 0.6895 (t-90) cc_final: 0.6468 (t-90) REVERT: C 904 TYR cc_start: 0.8113 (m-80) cc_final: 0.7770 (m-10) REVERT: M 13 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8476 (mm110) REVERT: M 59 TYR cc_start: 0.7928 (m-80) cc_final: 0.7556 (m-80) REVERT: M 72 ASP cc_start: 0.8792 (t0) cc_final: 0.8036 (t0) REVERT: M 75 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8848 (ptpp) REVERT: M 100 ASP cc_start: 0.8717 (t0) cc_final: 0.8314 (t0) REVERT: N 42 GLN cc_start: 0.8155 (pt0) cc_final: 0.7237 (pm20) REVERT: N 54 ARG cc_start: 0.7984 (ptp90) cc_final: 0.7484 (ptp90) REVERT: N 61 ARG cc_start: 0.8733 (ptt-90) cc_final: 0.8420 (ptt-90) REVERT: N 81 GLU cc_start: 0.8516 (pp20) cc_final: 0.8244 (pp20) REVERT: N 98 PHE cc_start: 0.7929 (m-80) cc_final: 0.7717 (m-80) outliers start: 61 outliers final: 50 residues processed: 335 average time/residue: 0.1886 time to fit residues: 102.0944 Evaluate side-chains 344 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 2 ASN Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 305 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 321 optimal weight: 0.5980 chunk 255 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 307 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.088158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057319 restraints weight = 78143.885| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.06 r_work: 0.2852 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30921 Z= 0.109 Angle : 0.532 11.217 42176 Z= 0.263 Chirality : 0.043 0.211 4858 Planarity : 0.003 0.047 5369 Dihedral : 4.876 53.582 5046 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.76 % Allowed : 10.50 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3705 helix: 2.48 (0.21), residues: 624 sheet: 0.33 (0.15), residues: 1026 loop : -0.19 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 19 TYR 0.027 0.001 TYR A 489 PHE 0.025 0.001 PHE M 67 TRP 0.020 0.001 TRP Y 35 HIS 0.004 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00251 (30829) covalent geometry : angle 0.52352 (41945) SS BOND : bond 0.00291 ( 45) SS BOND : angle 1.03330 ( 90) hydrogen bonds : bond 0.03298 ( 1205) hydrogen bonds : angle 4.97572 ( 3267) link_NAG-ASN : bond 0.00128 ( 47) link_NAG-ASN : angle 1.52795 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8305 (pmm) cc_final: 0.7956 (pmm) REVERT: B 394 ASN cc_start: 0.7795 (t0) cc_final: 0.7251 (t0) REVERT: B 402 ILE cc_start: 0.8739 (tt) cc_final: 0.8456 (tp) REVERT: B 531 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9128 (p) REVERT: X 64 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8558 (mmmm) REVERT: X 77 THR cc_start: 0.8392 (p) cc_final: 0.7338 (p) REVERT: X 79 TYR cc_start: 0.8769 (m-80) cc_final: 0.8161 (m-10) REVERT: X 82 MET cc_start: 0.8670 (mmt) cc_final: 0.8430 (mmt) REVERT: X 100 ASP cc_start: 0.9054 (t0) cc_final: 0.8765 (t0) REVERT: X 101 ASP cc_start: 0.8580 (p0) cc_final: 0.8368 (p0) REVERT: Y 2 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7920 (t0) REVERT: Y 11 LEU cc_start: 0.8099 (tp) cc_final: 0.7535 (tp) REVERT: Y 75 ILE cc_start: 0.8040 (mp) cc_final: 0.7419 (tp) REVERT: Y 77 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7382 (mtp85) REVERT: Y 79 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: Y 82 ASP cc_start: 0.7962 (m-30) cc_final: 0.7591 (m-30) REVERT: Y 100 GLN cc_start: 0.8836 (pm20) cc_final: 0.8415 (pm20) REVERT: Y 103 LYS cc_start: 0.9024 (tptp) cc_final: 0.8667 (tptp) REVERT: Y 105 GLU cc_start: 0.6584 (pt0) cc_final: 0.6151 (pm20) REVERT: A 52 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 586 ASP cc_start: 0.8606 (m-30) cc_final: 0.8309 (m-30) REVERT: H 4 LEU cc_start: 0.9137 (mm) cc_final: 0.8535 (mm) REVERT: H 23 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7779 (tm-30) REVERT: H 46 GLU cc_start: 0.8404 (tt0) cc_final: 0.7890 (tt0) REVERT: H 72 ASP cc_start: 0.8863 (t0) cc_final: 0.8206 (t0) REVERT: H 75 LYS cc_start: 0.9336 (mtmt) cc_final: 0.8714 (mtmt) REVERT: H 100 MET cc_start: 0.8748 (mpp) cc_final: 0.8412 (mpp) REVERT: H 105 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7987 (mm110) REVERT: L 24 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8579 (mmmt) REVERT: L 31 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8202 (t) REVERT: L 54 ARG cc_start: 0.8688 (ptp90) cc_final: 0.8312 (ptp90) REVERT: L 79 GLU cc_start: 0.7837 (mp0) cc_final: 0.7500 (mp0) REVERT: L 82 ASP cc_start: 0.8053 (m-30) cc_final: 0.7420 (m-30) REVERT: L 93 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8780 (pm20) REVERT: C 904 TYR cc_start: 0.8379 (m-80) cc_final: 0.8037 (m-10) REVERT: M 13 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8497 (mm110) REVERT: M 46 GLU cc_start: 0.8762 (tt0) cc_final: 0.8263 (tt0) REVERT: M 59 TYR cc_start: 0.7937 (m-80) cc_final: 0.7536 (m-80) REVERT: M 72 ASP cc_start: 0.8863 (t0) cc_final: 0.8138 (t0) REVERT: M 75 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8888 (ptpp) REVERT: M 100 ASP cc_start: 0.8864 (t0) cc_final: 0.8451 (t0) REVERT: N 42 GLN cc_start: 0.8163 (pt0) cc_final: 0.7226 (pm20) REVERT: N 54 ARG cc_start: 0.8007 (ptp90) cc_final: 0.7478 (ptp90) REVERT: N 61 ARG cc_start: 0.8741 (ptt-90) cc_final: 0.8422 (ptt-90) REVERT: N 81 GLU cc_start: 0.8537 (pp20) cc_final: 0.8254 (pp20) REVERT: N 98 PHE cc_start: 0.7952 (m-80) cc_final: 0.7391 (m-80) outliers start: 58 outliers final: 48 residues processed: 330 average time/residue: 0.1860 time to fit residues: 100.2179 Evaluate side-chains 338 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 2 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 201 optimal weight: 0.0980 chunk 107 optimal weight: 7.9990 chunk 337 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 297 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN Y 45 GLN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.086944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056218 restraints weight = 78760.327| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.13 r_work: 0.2813 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30921 Z= 0.133 Angle : 0.544 11.253 42176 Z= 0.269 Chirality : 0.044 0.215 4858 Planarity : 0.003 0.047 5369 Dihedral : 4.901 53.793 5046 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.73 % Allowed : 10.66 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3705 helix: 2.44 (0.21), residues: 624 sheet: 0.28 (0.15), residues: 1026 loop : -0.22 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 83 TYR 0.023 0.001 TYR A 489 PHE 0.020 0.001 PHE M 67 TRP 0.019 0.001 TRP Y 35 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00312 (30829) covalent geometry : angle 0.53565 (41945) SS BOND : bond 0.00309 ( 45) SS BOND : angle 1.12026 ( 90) hydrogen bonds : bond 0.03421 ( 1205) hydrogen bonds : angle 5.01254 ( 3267) link_NAG-ASN : bond 0.00114 ( 47) link_NAG-ASN : angle 1.54733 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10136.78 seconds wall clock time: 173 minutes 21.04 seconds (10401.04 seconds total)