Starting phenix.real_space_refine on Fri Jun 27 00:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y4c_38915/06_2025/8y4c_38915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y4c_38915/06_2025/8y4c_38915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y4c_38915/06_2025/8y4c_38915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y4c_38915/06_2025/8y4c_38915.map" model { file = "/net/cci-nas-00/data/ceres_data/8y4c_38915/06_2025/8y4c_38915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y4c_38915/06_2025/8y4c_38915.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 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 126 5.16 5 C 19761 2.51 5 N 5115 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.81s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31050 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 813 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "B" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 813 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 813 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "B" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 17.58, per 1000 atoms: 0.57 Number of scatterers: 31050 At special positions: 0 Unit cell: (164.32, 168.48, 185.12, 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 126 16.00 O 6048 8.00 N 5115 7.00 C 19761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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 B 840 " - pdb=" SG CYS B 851 " 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=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 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 E 22 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 245 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 354 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 657 " " NAG A1313 " - " ASN A 709 " " NAG A1314 " - " ASN A 717 " " NAG A1315 " - " ASN A 801 " " NAG A1316 " - " ASN A1074 " " NAG A1317 " - " ASN A1098 " " NAG A1318 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 245 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 354 " " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 709 " " NAG B1314 " - " ASN B 717 " " NAG B1315 " - " ASN B 801 " " NAG B1316 " - " ASN B1074 " " NAG B1317 " - " ASN B1098 " " NAG B1318 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 245 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 354 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1314 " - " ASN C 717 " " NAG C1315 " - " ASN C 801 " " NAG C1316 " - " ASN C1074 " " NAG C1317 " - " ASN C1098 " " NAG C1318 " - " ASN C1134 " Time building additional restraints: 7.29 Conformation dependent library (CDL) restraints added in 3.8 seconds 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7236 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 74 sheets defined 20.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.578A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.002A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.805A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 621 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.565A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.938A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.217A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.747A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.658A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.824A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.854A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.897A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.599A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.942A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.688A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 621 " --> 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 756 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.556A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 843 removed outlier: 3.980A pdb=" N ASP B 843 " --> pdb=" O CYS B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.522A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.240A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.746A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.807A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.980A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.878A pdb=" N THR D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.893A pdb=" N GLU F 85 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.601A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.998A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 623 removed outlier: 3.789A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER C 621 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.530A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.245A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.736A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.678A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.792A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.891A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.902A pdb=" N GLU G 85 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.773A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 55 removed outlier: 4.160A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.565A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.346A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.933A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.739A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.049A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.347A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.200A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.519A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.650A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.649A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.586A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.504A pdb=" N GLN H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.614A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC6, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.507A pdb=" N THR L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.955A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AC9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.781A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.603A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AD3, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.541A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.508A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.949A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.771A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.050A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.352A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.252A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AE5, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AE6, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.726A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.573A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.604A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.530A pdb=" N GLN D 79 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 74 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.533A pdb=" N TRP D 36 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG D 40 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.559A pdb=" N VAL F 18 " --> pdb=" O ILE F 77 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.916A pdb=" N TRP F 37 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AF7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.731A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.583A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.699A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.567A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.990A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AG5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG6, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.050A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AG8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.207A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 713 through 715 Processing sheet with id=AH1, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AH2, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.724A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.636A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.594A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AH6, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.622A pdb=" N GLN E 79 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP E 74 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.529A pdb=" N TRP E 36 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER E 52 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP E 38 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.509A pdb=" N THR G 23 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL G 18 " --> pdb=" O ILE G 77 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 9 through 12 removed outlier: 7.010A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 9 through 12 1072 hydrogen bonds defined for protein. 2802 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: 14.24 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9861 1.34 - 1.47: 8131 1.47 - 1.59: 13634 1.59 - 1.72: 3 1.72 - 1.84: 153 Bond restraints: 31782 Sorted by residual: bond pdb=" CB PRO C 631 " pdb=" CG PRO C 631 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.29e+00 bond pdb=" CB PRO B 631 " pdb=" CG PRO B 631 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.87e+00 bond pdb=" CB PRO A 631 " pdb=" CG PRO A 631 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.64e+00 bond pdb=" CB PRO A 85 " pdb=" CG PRO A 85 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.25e+00 bond pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta sigma weight residual 1.469 1.447 0.022 1.28e-02 6.10e+03 3.00e+00 ... (remaining 31777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 42860 3.14 - 6.29: 378 6.29 - 9.43: 33 9.43 - 12.58: 4 12.58 - 15.72: 6 Bond angle restraints: 43281 Sorted by residual: angle pdb=" CA PRO C 631 " pdb=" N PRO C 631 " pdb=" CD PRO C 631 " ideal model delta sigma weight residual 112.00 96.28 15.72 1.40e+00 5.10e-01 1.26e+02 angle pdb=" CA PRO B 631 " pdb=" N PRO B 631 " pdb=" CD PRO B 631 " ideal model delta sigma weight residual 112.00 96.82 15.18 1.40e+00 5.10e-01 1.18e+02 angle pdb=" CA PRO A 631 " pdb=" N PRO A 631 " pdb=" CD PRO A 631 " ideal model delta sigma weight residual 112.00 97.93 14.07 1.40e+00 5.10e-01 1.01e+02 angle pdb=" CA PRO A 85 " pdb=" N PRO A 85 " pdb=" CD PRO A 85 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.41e+01 angle pdb=" CA PRO C 85 " pdb=" N PRO C 85 " pdb=" CD PRO C 85 " ideal model delta sigma weight residual 112.00 104.21 7.79 1.40e+00 5.10e-01 3.09e+01 ... (remaining 43276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 16807 17.89 - 35.78: 2098 35.78 - 53.66: 533 53.66 - 71.55: 76 71.55 - 89.44: 31 Dihedral angle restraints: 19545 sinusoidal: 8253 harmonic: 11292 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 3.56 89.44 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 3.21 -89.21 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 2.75 -88.75 1 1.00e+01 1.00e-02 9.39e+01 ... (remaining 19542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3952 0.054 - 0.109: 932 0.109 - 0.163: 128 0.163 - 0.218: 20 0.218 - 0.272: 2 Chirality restraints: 5034 Sorted by residual: chirality pdb=" CB VAL A 570 " pdb=" CA VAL A 570 " pdb=" CG1 VAL A 570 " pdb=" CG2 VAL A 570 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL B1094 " pdb=" CA VAL B1094 " pdb=" CG1 VAL B1094 " pdb=" CG2 VAL B1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE C 896 " pdb=" CA ILE C 896 " pdb=" CG1 ILE C 896 " pdb=" CG2 ILE C 896 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 5031 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 630 " 0.143 5.00e-02 4.00e+02 2.02e-01 6.51e+01 pdb=" N PRO B 631 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO B 631 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO B 631 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 630 " 0.144 5.00e-02 4.00e+02 2.01e-01 6.49e+01 pdb=" N PRO C 631 " -0.347 5.00e-02 4.00e+02 pdb=" CA PRO C 631 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO C 631 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 630 " 0.139 5.00e-02 4.00e+02 1.98e-01 6.28e+01 pdb=" N PRO A 631 " -0.342 5.00e-02 4.00e+02 pdb=" CA PRO A 631 " 0.113 5.00e-02 4.00e+02 pdb=" CD PRO A 631 " 0.090 5.00e-02 4.00e+02 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 447 2.61 - 3.18: 28083 3.18 - 3.75: 47880 3.75 - 4.33: 64045 4.33 - 4.90: 107177 Nonbonded interactions: 247632 Sorted by model distance: nonbonded pdb=" OD2 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.035 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS C 590 " model vdw 2.088 3.040 nonbonded pdb=" O CYS B 590 " pdb=" OH TYR C 837 " model vdw 2.100 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.105 3.040 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR B 837 " model vdw 2.108 3.040 ... (remaining 247627 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 69.800 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.006 0.125 31881 Z= 0.249 Angle : 0.815 15.725 43533 Z= 0.429 Chirality : 0.048 0.272 5034 Planarity : 0.008 0.202 5514 Dihedral : 16.280 87.529 12174 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.37 % Favored : 91.32 % Rotamer: Outliers : 0.51 % Allowed : 29.17 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3858 helix: 0.57 (0.20), residues: 699 sheet: -0.46 (0.18), residues: 852 loop : -1.91 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 38 HIS 0.004 0.001 HIS L 36 PHE 0.019 0.002 PHE C 592 TYR 0.035 0.002 TYR C 904 ARG 0.008 0.001 ARG D 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 54) link_NAG-ASN : angle 1.74580 ( 162) hydrogen bonds : bond 0.21810 ( 1042) hydrogen bonds : angle 8.52065 ( 2802) SS BOND : bond 0.00428 ( 45) SS BOND : angle 1.58108 ( 90) covalent geometry : bond 0.00563 (31782) covalent geometry : angle 0.80687 (43281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 3.583 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: symmetry clash revert: symmetry clash REVERT: H 45 ARG cc_start: 0.6652 (mpp80) cc_final: 0.6428 (mpp80) REVERT: H 101 TRP cc_start: 0.8628 (t-100) cc_final: 0.7881 (t-100) REVERT: D 66 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8796 (ttmt) REVERT: G 34 ASP cc_start: 0.8147 (t70) cc_final: 0.7881 (m-30) outliers start: 17 outliers final: 10 residues processed: 273 average time/residue: 0.4150 time to fit residues: 187.8455 Evaluate side-chains 253 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 243 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain G residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 5.9990 chunk 293 optimal weight: 40.0000 chunk 162 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 303 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 351 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 658 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 339 HIS ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.123834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083452 restraints weight = 79823.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085991 restraints weight = 45400.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.087634 restraints weight = 32475.767| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31881 Z= 0.195 Angle : 0.698 9.127 43533 Z= 0.362 Chirality : 0.046 0.207 5034 Planarity : 0.006 0.141 5514 Dihedral : 6.382 56.166 5337 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.65 % Favored : 92.04 % Rotamer: Outliers : 3.54 % Allowed : 26.80 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3858 helix: 0.90 (0.20), residues: 705 sheet: -0.39 (0.17), residues: 921 loop : -1.98 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 38 HIS 0.003 0.001 HIS A 339 PHE 0.021 0.002 PHE C 970 TYR 0.023 0.002 TYR C 904 ARG 0.007 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 54) link_NAG-ASN : angle 1.65537 ( 162) hydrogen bonds : bond 0.04576 ( 1042) hydrogen bonds : angle 6.08884 ( 2802) SS BOND : bond 0.00527 ( 45) SS BOND : angle 1.24680 ( 90) covalent geometry : bond 0.00449 (31782) covalent geometry : angle 0.68993 (43281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 275 time to evaluate : 3.582 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 ARG cc_start: 0.3269 (OUTLIER) cc_final: 0.1787 (ttp-170) REVERT: H 6 GLU cc_start: 0.6937 (pm20) cc_final: 0.6643 (pm20) REVERT: H 22 CYS cc_start: 0.4880 (t) cc_final: 0.3993 (t) REVERT: H 35 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: H 38 TRP cc_start: 0.7929 (m100) cc_final: 0.7604 (m100) REVERT: H 48 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7085 (tm-30) REVERT: H 106 LEU cc_start: 0.8829 (mm) cc_final: 0.8579 (tp) REVERT: L 107 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7896 (mmmt) REVERT: B 495 TYR cc_start: -0.0626 (OUTLIER) cc_final: -0.2129 (m-80) REVERT: B 565 PHE cc_start: 0.8330 (t80) cc_final: 0.8000 (t80) REVERT: B 779 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8574 (tm-30) REVERT: D 35 TYR cc_start: 0.6087 (t80) cc_final: 0.5588 (t80) REVERT: D 38 TRP cc_start: 0.7835 (m100) cc_final: 0.6954 (m100) REVERT: D 45 ARG cc_start: 0.6770 (mpp80) cc_final: 0.6491 (mpp80) REVERT: F 17 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: F 47 LYS cc_start: 0.8088 (tttt) cc_final: 0.7863 (tttp) REVERT: C 462 LYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4743 (mttt) REVERT: C 945 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8112 (pp) outliers start: 119 outliers final: 66 residues processed: 365 average time/residue: 0.4277 time to fit residues: 259.3978 Evaluate side-chains 303 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 232 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 34 ASP Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 383 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 344 optimal weight: 0.0980 chunk 254 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 168 optimal weight: 30.0000 chunk 67 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 965 GLN A1083 HIS ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS C 755 GLN C 856 ASN C 965 GLN C1083 HIS ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.124223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084127 restraints weight = 79746.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086680 restraints weight = 45248.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088326 restraints weight = 32180.073| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31881 Z= 0.160 Angle : 0.651 11.689 43533 Z= 0.336 Chirality : 0.045 0.199 5034 Planarity : 0.006 0.117 5514 Dihedral : 5.751 52.751 5330 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.83 % Favored : 91.86 % Rotamer: Outliers : 3.83 % Allowed : 26.29 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 3858 helix: 1.02 (0.20), residues: 705 sheet: -0.29 (0.17), residues: 924 loop : -1.98 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS A1048 PHE 0.020 0.001 PHE C 970 TYR 0.021 0.001 TYR D 55 ARG 0.005 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 54) link_NAG-ASN : angle 1.54443 ( 162) hydrogen bonds : bond 0.04176 ( 1042) hydrogen bonds : angle 5.58731 ( 2802) SS BOND : bond 0.00419 ( 45) SS BOND : angle 1.12461 ( 90) covalent geometry : bond 0.00367 (31782) covalent geometry : angle 0.64406 (43281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 286 time to evaluate : 3.329 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: symmetry clash REVERT: A 565 PHE cc_start: 0.8397 (t80) cc_final: 0.7823 (t80) REVERT: A 707 TYR cc_start: 0.8057 (t80) cc_final: 0.7748 (t80) REVERT: A 847 ARG cc_start: 0.3432 (OUTLIER) cc_final: 0.1814 (ttp-170) REVERT: H 22 CYS cc_start: 0.4817 (t) cc_final: 0.3876 (t) REVERT: H 35 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: H 38 TRP cc_start: 0.7850 (m100) cc_final: 0.7493 (m100) REVERT: H 48 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7066 (tm-30) REVERT: H 112 TRP cc_start: 0.8576 (p90) cc_final: 0.8234 (p90) REVERT: L 16 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6136 (pt0) REVERT: L 87 GLU cc_start: 0.8188 (tp30) cc_final: 0.7000 (tp30) REVERT: L 107 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8088 (tppt) REVERT: B 774 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7794 (mm-40) REVERT: B 779 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 847 ARG cc_start: 0.2855 (OUTLIER) cc_final: 0.1877 (ttp-170) REVERT: B 873 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: D 35 TYR cc_start: 0.6241 (t80) cc_final: 0.5791 (t80) REVERT: D 45 ARG cc_start: 0.6736 (mpp80) cc_final: 0.6360 (mpp80) REVERT: F 16 GLN cc_start: 0.6376 (OUTLIER) cc_final: 0.6038 (pt0) REVERT: F 17 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7634 (mmm-85) REVERT: F 47 LYS cc_start: 0.8006 (tttt) cc_final: 0.7781 (tttp) REVERT: C 238 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7830 (t80) REVERT: C 462 LYS cc_start: 0.5295 (OUTLIER) cc_final: 0.4960 (mttt) REVERT: C 945 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8190 (pp) REVERT: E 6 GLU cc_start: 0.5539 (pm20) cc_final: 0.5214 (pm20) REVERT: E 13 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8438 (mmmt) REVERT: E 118 GLN cc_start: 0.6932 (pm20) cc_final: 0.6379 (pm20) REVERT: G 16 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6288 (pt0) outliers start: 129 outliers final: 66 residues processed: 396 average time/residue: 0.3816 time to fit residues: 252.5920 Evaluate side-chains 327 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 251 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain F residue 16 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 34 ASP Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 13 optimal weight: 0.5980 chunk 352 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 167 optimal weight: 40.0000 chunk 205 optimal weight: 0.6980 chunk 376 optimal weight: 0.0270 chunk 290 optimal weight: 9.9990 chunk 170 optimal weight: 50.0000 chunk 349 optimal weight: 3.9990 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 965 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 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 = 0.3987 r_free = 0.3987 target = 0.124859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085151 restraints weight = 79628.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087644 restraints weight = 45701.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089264 restraints weight = 32766.101| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31881 Z= 0.133 Angle : 0.638 11.476 43533 Z= 0.326 Chirality : 0.045 0.196 5034 Planarity : 0.005 0.111 5514 Dihedral : 5.410 54.138 5330 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.72 % Favored : 91.96 % Rotamer: Outliers : 3.36 % Allowed : 26.89 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3858 helix: 1.10 (0.20), residues: 708 sheet: -0.26 (0.17), residues: 918 loop : -1.94 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 38 HIS 0.004 0.001 HIS L 36 PHE 0.015 0.001 PHE A 592 TYR 0.026 0.001 TYR E 55 ARG 0.007 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 54) link_NAG-ASN : angle 1.50945 ( 162) hydrogen bonds : bond 0.03771 ( 1042) hydrogen bonds : angle 5.36768 ( 2802) SS BOND : bond 0.00400 ( 45) SS BOND : angle 1.10119 ( 90) covalent geometry : bond 0.00305 (31782) covalent geometry : angle 0.63082 (43281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 291 time to evaluate : 3.684 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: symmetry clash REVERT: A 294 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 565 PHE cc_start: 0.8120 (t80) cc_final: 0.7459 (t80) REVERT: A 707 TYR cc_start: 0.8071 (t80) cc_final: 0.7863 (t80) REVERT: A 847 ARG cc_start: 0.2948 (OUTLIER) cc_final: 0.1620 (ttp-170) REVERT: A 981 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7154 (pp) REVERT: H 2 LEU cc_start: 0.8527 (mm) cc_final: 0.8195 (mm) REVERT: H 22 CYS cc_start: 0.4884 (t) cc_final: 0.3881 (t) REVERT: H 35 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: H 38 TRP cc_start: 0.7775 (m100) cc_final: 0.7085 (m100) REVERT: H 101 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.7959 (t-100) REVERT: H 112 TRP cc_start: 0.8556 (p90) cc_final: 0.8229 (p90) REVERT: L 16 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.6107 (pt0) REVERT: L 87 GLU cc_start: 0.8118 (tp30) cc_final: 0.7283 (tp30) REVERT: L 107 LYS cc_start: 0.8470 (mmmt) cc_final: 0.7905 (mmmt) REVERT: B 565 PHE cc_start: 0.8150 (t80) cc_final: 0.7780 (t80) REVERT: B 774 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7867 (mm-40) REVERT: B 779 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8467 (tm-30) REVERT: B 847 ARG cc_start: 0.2563 (OUTLIER) cc_final: 0.1535 (ttp-170) REVERT: B 873 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 981 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6745 (pp) REVERT: D 35 TYR cc_start: 0.6226 (t80) cc_final: 0.5821 (t80) REVERT: D 55 TYR cc_start: 0.8452 (p90) cc_final: 0.8149 (p90) REVERT: C 462 LYS cc_start: 0.5290 (OUTLIER) cc_final: 0.4965 (mttt) REVERT: C 756 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6406 (m-10) REVERT: C 945 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8215 (pp) REVERT: E 118 GLN cc_start: 0.6948 (pm20) cc_final: 0.6628 (pm20) REVERT: G 16 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6255 (pt0) REVERT: G 107 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7917 (mmmt) outliers start: 113 outliers final: 62 residues processed: 377 average time/residue: 0.3909 time to fit residues: 246.2445 Evaluate side-chains 337 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 262 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 34 ASP Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 310 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 357 optimal weight: 2.9990 chunk 204 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 23 optimal weight: 0.2980 chunk 263 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 965 GLN C1142 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 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 = 0.3994 r_free = 0.3994 target = 0.124735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084057 restraints weight = 78627.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086664 restraints weight = 45046.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088284 restraints weight = 32346.024| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31881 Z= 0.120 Angle : 0.638 12.950 43533 Z= 0.323 Chirality : 0.045 0.215 5034 Planarity : 0.005 0.102 5514 Dihedral : 5.080 55.734 5328 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.59 % Favored : 92.09 % Rotamer: Outliers : 3.65 % Allowed : 27.06 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3858 helix: 1.15 (0.19), residues: 708 sheet: -0.25 (0.17), residues: 921 loop : -1.88 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 112 HIS 0.004 0.000 HIS F 36 PHE 0.014 0.001 PHE A 592 TYR 0.017 0.001 TYR H 60 ARG 0.005 0.000 ARG H 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 54) link_NAG-ASN : angle 1.46073 ( 162) hydrogen bonds : bond 0.03640 ( 1042) hydrogen bonds : angle 5.23021 ( 2802) SS BOND : bond 0.00451 ( 45) SS BOND : angle 1.36949 ( 90) covalent geometry : bond 0.00276 (31782) covalent geometry : angle 0.63000 (43281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 307 time to evaluate : 3.311 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: A 294 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7985 (t0) REVERT: A 565 PHE cc_start: 0.7995 (t80) cc_final: 0.7349 (t80) REVERT: A 847 ARG cc_start: 0.2912 (OUTLIER) cc_final: 0.1647 (ttp-170) REVERT: A 981 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7128 (pp) REVERT: A 1002 GLN cc_start: 0.8192 (mm110) cc_final: 0.7927 (tm-30) REVERT: H 35 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: H 48 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7217 (tm-30) REVERT: H 101 TRP cc_start: 0.8262 (OUTLIER) cc_final: 0.7982 (t-100) REVERT: H 112 TRP cc_start: 0.8420 (p90) cc_final: 0.8171 (p90) REVERT: L 87 GLU cc_start: 0.8118 (tp30) cc_final: 0.7575 (tp30) REVERT: L 107 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8178 (mmmt) REVERT: B 779 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8450 (tm-30) REVERT: B 847 ARG cc_start: 0.2368 (OUTLIER) cc_final: 0.1401 (ttt-90) REVERT: B 873 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: B 981 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6639 (pp) REVERT: D 35 TYR cc_start: 0.6176 (t80) cc_final: 0.5749 (t80) REVERT: D 55 TYR cc_start: 0.8457 (p90) cc_final: 0.8190 (p90) REVERT: C 462 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.5066 (mttt) REVERT: C 756 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6365 (m-10) REVERT: C 945 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8282 (pp) REVERT: E 112 TRP cc_start: 0.8562 (p90) cc_final: 0.8279 (p90) outliers start: 123 outliers final: 73 residues processed: 399 average time/residue: 0.3989 time to fit residues: 266.3584 Evaluate side-chains 346 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 34 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 53 optimal weight: 0.1980 chunk 30 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 329 optimal weight: 0.0030 chunk 377 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 965 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 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 = 0.4011 r_free = 0.4011 target = 0.126274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086780 restraints weight = 79905.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089345 restraints weight = 45432.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.090955 restraints weight = 32427.648| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31881 Z= 0.115 Angle : 0.647 14.935 43533 Z= 0.327 Chirality : 0.045 0.232 5034 Planarity : 0.005 0.093 5514 Dihedral : 4.915 56.432 5327 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.13 % Favored : 92.56 % Rotamer: Outliers : 3.71 % Allowed : 26.89 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 3858 helix: 1.17 (0.19), residues: 711 sheet: -0.15 (0.17), residues: 909 loop : -1.83 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 112 HIS 0.003 0.000 HIS B1048 PHE 0.018 0.001 PHE A 392 TYR 0.028 0.001 TYR E 55 ARG 0.004 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 54) link_NAG-ASN : angle 1.42424 ( 162) hydrogen bonds : bond 0.03485 ( 1042) hydrogen bonds : angle 5.10728 ( 2802) SS BOND : bond 0.00381 ( 45) SS BOND : angle 1.32023 ( 90) covalent geometry : bond 0.00260 (31782) covalent geometry : angle 0.64003 (43281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 283 time to evaluate : 3.389 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7937 (t0) REVERT: A 565 PHE cc_start: 0.7840 (t80) cc_final: 0.7159 (t80) REVERT: A 847 ARG cc_start: 0.2840 (OUTLIER) cc_final: 0.1591 (ttp-170) REVERT: A 981 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7070 (pp) REVERT: A 1002 GLN cc_start: 0.8198 (mm110) cc_final: 0.7965 (tm-30) REVERT: H 35 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: H 48 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7212 (tm-30) REVERT: H 101 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7981 (t-100) REVERT: H 112 TRP cc_start: 0.8434 (p90) cc_final: 0.8179 (p90) REVERT: L 87 GLU cc_start: 0.8088 (tp30) cc_final: 0.7412 (tp30) REVERT: L 107 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8148 (mmmt) REVERT: B 634 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7965 (ptt180) REVERT: B 779 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8405 (tm-30) REVERT: B 873 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 981 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6681 (pp) REVERT: B 1002 GLN cc_start: 0.8375 (mm110) cc_final: 0.8108 (tm-30) REVERT: D 35 TYR cc_start: 0.6166 (t80) cc_final: 0.5908 (t80) REVERT: D 38 TRP cc_start: 0.7464 (m100) cc_final: 0.6615 (m100) REVERT: C 462 LYS cc_start: 0.5289 (OUTLIER) cc_final: 0.5001 (mttt) REVERT: C 756 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6347 (m-10) REVERT: C 900 MET cc_start: 0.7524 (mtp) cc_final: 0.7245 (mtp) REVERT: C 945 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8316 (pp) REVERT: C 1002 GLN cc_start: 0.8198 (mm110) cc_final: 0.7758 (tm-30) REVERT: G 107 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7992 (mmmt) outliers start: 125 outliers final: 80 residues processed: 378 average time/residue: 0.4153 time to fit residues: 261.6591 Evaluate side-chains 358 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 267 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 34 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 6 optimal weight: 0.0020 chunk 325 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 297 optimal weight: 0.6980 chunk 310 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 245 optimal weight: 3.9990 overall best weight: 1.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 965 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 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 = 0.3977 r_free = 0.3977 target = 0.123576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.082428 restraints weight = 78704.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085025 restraints weight = 44588.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086709 restraints weight = 31839.072| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31881 Z= 0.164 Angle : 0.659 12.119 43533 Z= 0.334 Chirality : 0.045 0.209 5034 Planarity : 0.005 0.088 5514 Dihedral : 4.969 57.632 5327 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.22 % Favored : 91.47 % Rotamer: Outliers : 3.77 % Allowed : 27.27 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3858 helix: 1.13 (0.20), residues: 711 sheet: -0.40 (0.16), residues: 969 loop : -1.86 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 112 HIS 0.002 0.001 HIS A1048 PHE 0.017 0.001 PHE B1121 TYR 0.026 0.001 TYR D 60 ARG 0.006 0.000 ARG G 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 54) link_NAG-ASN : angle 1.45610 ( 162) hydrogen bonds : bond 0.03740 ( 1042) hydrogen bonds : angle 5.13868 ( 2802) SS BOND : bond 0.00609 ( 45) SS BOND : angle 1.49844 ( 90) covalent geometry : bond 0.00388 (31782) covalent geometry : angle 0.65098 (43281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 282 time to evaluate : 3.368 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.0164 (OUTLIER) cc_final: -0.0634 (m-80) REVERT: A 565 PHE cc_start: 0.8219 (t80) cc_final: 0.7593 (t80) REVERT: A 756 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: A 847 ARG cc_start: 0.2917 (OUTLIER) cc_final: 0.1700 (ttp-170) REVERT: A 981 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7108 (pp) REVERT: H 35 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: H 38 TRP cc_start: 0.8047 (m100) cc_final: 0.7393 (m100) REVERT: H 101 TRP cc_start: 0.8308 (OUTLIER) cc_final: 0.7931 (t-100) REVERT: H 112 TRP cc_start: 0.8509 (p90) cc_final: 0.8156 (p90) REVERT: L 16 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6095 (pt0) REVERT: L 17 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7624 (mmm-85) REVERT: L 32 ARG cc_start: 0.8905 (tpp80) cc_final: 0.8655 (tpp80) REVERT: L 56 ARG cc_start: 0.8268 (ptp-170) cc_final: 0.7957 (ptt-90) REVERT: L 87 GLU cc_start: 0.8105 (tp30) cc_final: 0.7550 (tp30) REVERT: L 107 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8357 (mmmt) REVERT: B 634 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8055 (ptt180) REVERT: B 756 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6341 (m-10) REVERT: B 779 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 856 ASN cc_start: 0.7546 (t0) cc_final: 0.7298 (t0) REVERT: B 873 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: B 981 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6665 (pp) REVERT: B 1002 GLN cc_start: 0.8418 (mm110) cc_final: 0.8189 (tm-30) REVERT: D 35 TYR cc_start: 0.6246 (t80) cc_final: 0.5958 (t80) REVERT: D 38 TRP cc_start: 0.7629 (m100) cc_final: 0.6799 (m100) REVERT: F 75 LEU cc_start: 0.8378 (tp) cc_final: 0.8144 (tp) REVERT: F 87 GLU cc_start: 0.8431 (tp30) cc_final: 0.8149 (tp30) REVERT: F 107 LYS cc_start: 0.8373 (mmmt) cc_final: 0.7903 (mmmt) REVERT: C 462 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.5007 (mttt) REVERT: C 634 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7910 (ptt-90) REVERT: C 756 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6341 (m-10) REVERT: C 945 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8366 (pp) REVERT: C 1002 GLN cc_start: 0.8194 (mm110) cc_final: 0.7804 (tm-30) REVERT: G 16 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6397 (pt0) REVERT: G 20 ILE cc_start: 0.8572 (mm) cc_final: 0.8114 (mm) REVERT: G 107 LYS cc_start: 0.8217 (mmmt) cc_final: 0.8012 (mmmt) outliers start: 127 outliers final: 86 residues processed: 384 average time/residue: 0.4075 time to fit residues: 255.4441 Evaluate side-chains 368 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 266 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 380 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 346 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 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 = 0.3937 r_free = 0.3937 target = 0.121124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079711 restraints weight = 79119.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082201 restraints weight = 45387.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.083824 restraints weight = 32702.168| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31881 Z= 0.250 Angle : 0.726 13.117 43533 Z= 0.370 Chirality : 0.048 0.248 5034 Planarity : 0.005 0.096 5514 Dihedral : 5.428 58.928 5327 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.84 % Favored : 90.85 % Rotamer: Outliers : 3.65 % Allowed : 27.66 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 3858 helix: 0.97 (0.20), residues: 711 sheet: -0.56 (0.17), residues: 954 loop : -1.98 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 112 HIS 0.005 0.001 HIS B 519 PHE 0.021 0.002 PHE B1121 TYR 0.039 0.002 TYR D 60 ARG 0.007 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 54) link_NAG-ASN : angle 1.58781 ( 162) hydrogen bonds : bond 0.04209 ( 1042) hydrogen bonds : angle 5.36045 ( 2802) SS BOND : bond 0.00620 ( 45) SS BOND : angle 1.66367 ( 90) covalent geometry : bond 0.00591 (31782) covalent geometry : angle 0.71781 (43281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 262 time to evaluate : 3.499 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.0157 (OUTLIER) cc_final: -0.0873 (m-80) REVERT: A 565 PHE cc_start: 0.8466 (t80) cc_final: 0.7926 (t80) REVERT: A 756 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: A 847 ARG cc_start: 0.3115 (OUTLIER) cc_final: 0.2073 (ttp-170) REVERT: A 1136 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8881 (t) REVERT: H 35 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: H 48 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7191 (tm-30) REVERT: H 101 TRP cc_start: 0.8408 (OUTLIER) cc_final: 0.7727 (t-100) REVERT: H 112 TRP cc_start: 0.8687 (p90) cc_final: 0.8146 (p90) REVERT: L 16 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6257 (pt0) REVERT: L 32 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8745 (tpp80) REVERT: L 87 GLU cc_start: 0.8126 (tp30) cc_final: 0.7547 (tp30) REVERT: L 107 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8367 (mmmt) REVERT: B 756 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6524 (m-10) REVERT: B 779 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8464 (tm-30) REVERT: B 873 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: D 55 TYR cc_start: 0.8443 (p90) cc_final: 0.8116 (p90) REVERT: C 238 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.7845 (t80) REVERT: C 462 LYS cc_start: 0.5264 (OUTLIER) cc_final: 0.4921 (mttt) REVERT: C 756 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6368 (m-10) REVERT: C 945 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8450 (pp) REVERT: G 16 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6575 (pt0) REVERT: G 20 ILE cc_start: 0.8633 (mm) cc_final: 0.8180 (mm) outliers start: 123 outliers final: 88 residues processed: 362 average time/residue: 0.4136 time to fit residues: 247.0808 Evaluate side-chains 338 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 236 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 71 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 344 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 318 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 308 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 367 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1036 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 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 = 0.3985 r_free = 0.3985 target = 0.124112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083207 restraints weight = 78673.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085829 restraints weight = 44274.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087497 restraints weight = 31551.622| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31881 Z= 0.122 Angle : 0.670 13.344 43533 Z= 0.336 Chirality : 0.045 0.191 5034 Planarity : 0.005 0.097 5514 Dihedral : 5.000 59.642 5327 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.83 % Favored : 91.86 % Rotamer: Outliers : 2.67 % Allowed : 29.08 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3858 helix: 1.14 (0.20), residues: 711 sheet: -0.50 (0.17), residues: 963 loop : -1.90 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP E 112 HIS 0.003 0.001 HIS A1048 PHE 0.011 0.001 PHE A 898 TYR 0.020 0.001 TYR E 35 ARG 0.006 0.000 ARG G 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 54) link_NAG-ASN : angle 1.42358 ( 162) hydrogen bonds : bond 0.03533 ( 1042) hydrogen bonds : angle 5.09571 ( 2802) SS BOND : bond 0.00509 ( 45) SS BOND : angle 1.48499 ( 90) covalent geometry : bond 0.00282 (31782) covalent geometry : angle 0.66263 (43281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 282 time to evaluate : 3.740 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: symmetry clash 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: symmetry clash REVERT: A 495 TYR cc_start: 0.0052 (OUTLIER) cc_final: -0.0987 (m-80) REVERT: A 565 PHE cc_start: 0.7998 (t80) cc_final: 0.7348 (t80) REVERT: A 847 ARG cc_start: 0.2849 (OUTLIER) cc_final: 0.1857 (ttp-170) REVERT: A 981 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6865 (pp) REVERT: A 993 ILE cc_start: 0.8212 (pt) cc_final: 0.8011 (mt) REVERT: H 35 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: H 101 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7755 (t-100) REVERT: H 112 TRP cc_start: 0.8472 (p90) cc_final: 0.8146 (p90) REVERT: L 16 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6232 (pt0) REVERT: L 32 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8677 (tpp80) REVERT: L 87 GLU cc_start: 0.8098 (tp30) cc_final: 0.6950 (tp30) REVERT: B 565 PHE cc_start: 0.7960 (t80) cc_final: 0.7694 (t80) REVERT: B 756 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6339 (m-10) REVERT: B 779 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8426 (tm-30) REVERT: B 873 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: B 981 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6619 (pp) REVERT: D 38 TRP cc_start: 0.7642 (m100) cc_final: 0.6834 (m100) REVERT: D 55 TYR cc_start: 0.8369 (p90) cc_final: 0.8091 (p90) REVERT: C 462 LYS cc_start: 0.5313 (OUTLIER) cc_final: 0.4985 (mttt) REVERT: C 756 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6334 (m-10) REVERT: G 20 ILE cc_start: 0.8556 (mm) cc_final: 0.8168 (mm) REVERT: G 34 ASP cc_start: 0.8269 (t70) cc_final: 0.7971 (t0) outliers start: 90 outliers final: 66 residues processed: 353 average time/residue: 0.5697 time to fit residues: 333.7872 Evaluate side-chains 342 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 265 time to evaluate : 5.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 102 optimal weight: 1.9990 chunk 349 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 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 = 0.3967 r_free = 0.3967 target = 0.122978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082232 restraints weight = 79093.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084746 restraints weight = 45711.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086364 restraints weight = 32956.277| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31881 Z= 0.162 Angle : 0.686 13.320 43533 Z= 0.344 Chirality : 0.046 0.193 5034 Planarity : 0.005 0.097 5514 Dihedral : 4.972 59.244 5327 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.01 % Favored : 91.68 % Rotamer: Outliers : 2.85 % Allowed : 28.82 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 3858 helix: 1.11 (0.20), residues: 711 sheet: -0.49 (0.16), residues: 978 loop : -1.88 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP E 112 HIS 0.002 0.001 HIS A1048 PHE 0.014 0.001 PHE B1121 TYR 0.027 0.001 TYR D 60 ARG 0.006 0.000 ARG L 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 54) link_NAG-ASN : angle 1.46957 ( 162) hydrogen bonds : bond 0.03707 ( 1042) hydrogen bonds : angle 5.11968 ( 2802) SS BOND : bond 0.00506 ( 45) SS BOND : angle 1.28179 ( 90) covalent geometry : bond 0.00385 (31782) covalent geometry : angle 0.67978 (43281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 262 time to evaluate : 3.423 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.0097 (OUTLIER) cc_final: -0.1101 (m-80) REVERT: A 565 PHE cc_start: 0.8167 (t80) cc_final: 0.7511 (t80) REVERT: A 847 ARG cc_start: 0.3158 (OUTLIER) cc_final: 0.2183 (ttp-170) REVERT: A 981 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6998 (pp) REVERT: H 35 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: H 48 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7212 (tm-30) REVERT: H 101 TRP cc_start: 0.8361 (OUTLIER) cc_final: 0.7780 (t-100) REVERT: H 112 TRP cc_start: 0.8566 (p90) cc_final: 0.8163 (p90) REVERT: L 16 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6340 (pt0) REVERT: L 32 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8672 (tpp80) REVERT: B 565 PHE cc_start: 0.8188 (t80) cc_final: 0.7906 (t80) REVERT: B 756 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: B 779 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 847 ARG cc_start: 0.2566 (OUTLIER) cc_final: 0.1915 (ttp-170) REVERT: B 873 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: D 38 TRP cc_start: 0.7703 (m100) cc_final: 0.6897 (m100) REVERT: D 55 TYR cc_start: 0.8381 (p90) cc_final: 0.8097 (p90) REVERT: F 56 ARG cc_start: 0.8295 (ptp-170) cc_final: 0.7997 (ptt-90) REVERT: C 462 LYS cc_start: 0.5265 (OUTLIER) cc_final: 0.4919 (mttt) REVERT: C 756 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6348 (m-10) REVERT: E 101 TRP cc_start: 0.8105 (OUTLIER) cc_final: 0.7743 (t-100) REVERT: G 20 ILE cc_start: 0.8601 (mm) cc_final: 0.8168 (mm) REVERT: G 34 ASP cc_start: 0.8264 (t70) cc_final: 0.7911 (t0) outliers start: 96 outliers final: 72 residues processed: 337 average time/residue: 0.4008 time to fit residues: 222.4148 Evaluate side-chains 334 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 250 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 129 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 224 optimal weight: 0.3980 chunk 153 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 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 = 0.3951 r_free = 0.3951 target = 0.121932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080888 restraints weight = 78802.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083441 restraints weight = 45114.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085060 restraints weight = 32365.995| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31881 Z= 0.198 Angle : 0.716 13.333 43533 Z= 0.359 Chirality : 0.047 0.198 5034 Planarity : 0.005 0.097 5514 Dihedral : 5.122 57.486 5327 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.29 % Favored : 91.37 % Rotamer: Outliers : 2.85 % Allowed : 29.00 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3858 helix: 1.07 (0.20), residues: 711 sheet: -0.50 (0.17), residues: 960 loop : -1.95 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP E 112 HIS 0.002 0.001 HIS A1048 PHE 0.016 0.001 PHE B1121 TYR 0.031 0.002 TYR D 60 ARG 0.008 0.000 ARG G 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 54) link_NAG-ASN : angle 1.51528 ( 162) hydrogen bonds : bond 0.03912 ( 1042) hydrogen bonds : angle 5.22381 ( 2802) SS BOND : bond 0.00658 ( 45) SS BOND : angle 1.42929 ( 90) covalent geometry : bond 0.00468 (31782) covalent geometry : angle 0.70873 (43281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11271.93 seconds wall clock time: 197 minutes 32.13 seconds (11852.13 seconds total)