Starting phenix.real_space_refine on Mon Aug 25 22:18:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y4c_38915/08_2025/8y4c_38915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y4c_38915/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y4c_38915/08_2025/8y4c_38915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y4c_38915/08_2025/8y4c_38915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y4c_38915/08_2025/8y4c_38915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y4c_38915/08_2025/8y4c_38915.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.76, per 1000 atoms: 0.22 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.23 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: 7.46 Time building geometry restraints manager: 3.38 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: 0.02 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: 1.970 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.130 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG D 45 TYR 0.035 0.002 TYR C 904 PHE 0.019 0.002 PHE C 592 TRP 0.056 0.002 TRP E 38 HIS 0.004 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00563 (31782) covalent geometry : angle 0.80687 (43281) SS BOND : bond 0.00428 ( 45) SS BOND : angle 1.58108 ( 90) hydrogen bonds : bond 0.21810 ( 1042) hydrogen bonds : angle 8.52065 ( 2802) link_NAG-ASN : bond 0.00177 ( 54) link_NAG-ASN : angle 1.74580 ( 162) *********************** 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 : 1.236 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: 0.7880 (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: 0.7880 (m-30) outliers start: 17 outliers final: 10 residues processed: 273 average time/residue: 0.1726 time to fit residues: 78.2356 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 : 1.043 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0010 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 339 HIS C 755 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.123209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081745 restraints weight = 79440.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.084348 restraints weight = 45055.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085956 restraints weight = 32254.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086985 restraints weight = 26542.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087506 restraints weight = 23621.497| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31881 Z= 0.193 Angle : 0.695 9.122 43533 Z= 0.360 Chirality : 0.046 0.201 5034 Planarity : 0.006 0.143 5514 Dihedral : 6.409 56.706 5337 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.47 % Favored : 92.22 % Rotamer: Outliers : 3.51 % Allowed : 26.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.13), residues: 3858 helix: 0.90 (0.20), residues: 705 sheet: -0.39 (0.17), residues: 921 loop : -1.97 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 995 TYR 0.022 0.002 TYR E 55 PHE 0.021 0.001 PHE C 970 TRP 0.018 0.001 TRP E 38 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00438 (31782) covalent geometry : angle 0.68711 (43281) SS BOND : bond 0.00639 ( 45) SS BOND : angle 1.24539 ( 90) hydrogen bonds : bond 0.04900 ( 1042) hydrogen bonds : angle 6.16549 ( 2802) link_NAG-ASN : bond 0.00232 ( 54) link_NAG-ASN : angle 1.66177 ( 162) *********************** 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 395 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 277 time to evaluate : 0.761 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 847 ARG cc_start: 0.3199 (OUTLIER) cc_final: 0.1707 (ttp-170) REVERT: H 6 GLU cc_start: 0.6921 (pm20) cc_final: 0.6642 (pm20) REVERT: H 22 CYS cc_start: 0.4869 (t) cc_final: 0.4006 (t) REVERT: H 35 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: H 38 TRP cc_start: 0.7932 (m100) cc_final: 0.7613 (m100) REVERT: H 48 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7077 (tm-30) REVERT: H 106 LEU cc_start: 0.8807 (mm) cc_final: 0.8562 (tp) REVERT: L 107 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7918 (mmmt) REVERT: B 495 TYR cc_start: -0.0646 (OUTLIER) cc_final: -0.2153 (m-80) REVERT: B 565 PHE cc_start: 0.8346 (t80) cc_final: 0.8029 (t80) REVERT: D 35 TYR cc_start: 0.6064 (t80) cc_final: 0.5515 (t80) REVERT: F 17 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7602 (mmm-85) REVERT: F 47 LYS cc_start: 0.8081 (tttt) cc_final: 0.7857 (tttp) REVERT: C 462 LYS cc_start: 0.5096 (OUTLIER) cc_final: 0.4751 (mttt) REVERT: C 945 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8034 (pp) REVERT: G 85 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7818 (tm-30) outliers start: 118 outliers final: 65 residues processed: 364 average time/residue: 0.1696 time to fit residues: 101.3032 Evaluate side-chains 311 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 B residue 1142 GLN 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 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 330 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 382 optimal weight: 0.0970 chunk 16 optimal weight: 7.9990 chunk 300 optimal weight: 0.0370 chunk 265 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- 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 A 856 ASN A1083 HIS ** 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 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 856 ASN C 965 GLN C1083 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.125377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087382 restraints weight = 79868.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089463 restraints weight = 48848.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089601 restraints weight = 33032.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089989 restraints weight = 33437.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090093 restraints weight = 31099.285| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31881 Z= 0.130 Angle : 0.644 11.882 43533 Z= 0.331 Chirality : 0.045 0.196 5034 Planarity : 0.006 0.119 5514 Dihedral : 5.733 51.103 5330 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.54 % Favored : 92.15 % Rotamer: Outliers : 3.09 % Allowed : 26.83 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.13), residues: 3858 helix: 1.04 (0.19), residues: 705 sheet: -0.33 (0.17), residues: 936 loop : -1.94 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.021 0.001 TYR D 55 PHE 0.020 0.001 PHE C 970 TRP 0.012 0.001 TRP E 38 HIS 0.002 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00295 (31782) covalent geometry : angle 0.63772 (43281) SS BOND : bond 0.00381 ( 45) SS BOND : angle 1.08754 ( 90) hydrogen bonds : bond 0.04072 ( 1042) hydrogen bonds : angle 5.62347 ( 2802) link_NAG-ASN : bond 0.00163 ( 54) link_NAG-ASN : angle 1.50579 ( 162) *********************** 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 396 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 292 time to evaluate : 1.024 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: A 565 PHE cc_start: 0.8245 (t80) cc_final: 0.7636 (t80) REVERT: A 707 TYR cc_start: 0.7943 (t80) cc_final: 0.7648 (t80) REVERT: A 847 ARG cc_start: 0.3371 (OUTLIER) cc_final: 0.1733 (ttp-170) REVERT: A 1107 ARG cc_start: 0.7535 (mmm-85) cc_final: 0.7249 (mmt90) REVERT: H 22 CYS cc_start: 0.5060 (t) cc_final: 0.3967 (t) REVERT: H 35 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: H 38 TRP cc_start: 0.7866 (m100) cc_final: 0.7480 (m100) REVERT: H 48 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7053 (tm-30) REVERT: H 112 TRP cc_start: 0.8514 (p90) cc_final: 0.8179 (p90) REVERT: L 87 GLU cc_start: 0.8227 (tp30) cc_final: 0.7496 (tp30) REVERT: L 107 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7937 (mmmt) REVERT: B 565 PHE cc_start: 0.8052 (t80) cc_final: 0.7674 (t80) REVERT: B 779 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 873 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: D 35 TYR cc_start: 0.6061 (t80) cc_final: 0.5565 (t80) REVERT: D 45 ARG cc_start: 0.6693 (mpp80) cc_final: 0.6424 (mpp80) REVERT: C 462 LYS cc_start: 0.5083 (OUTLIER) cc_final: 0.4719 (mttt) REVERT: C 945 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8200 (pp) REVERT: E 13 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8501 (mmmt) outliers start: 104 outliers final: 49 residues processed: 371 average time/residue: 0.1664 time to fit residues: 103.5086 Evaluate side-chains 309 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR 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 847 ARG Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1141 LEU 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 101 VAL Chi-restraints excluded: chain B residue 51 THR 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 752 LEU 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 1141 LEU Chi-restraints excluded: chain D residue 47 LEU 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 50 LEU Chi-restraints excluded: chain C residue 166 CYS 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 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 760 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1141 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 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 126 optimal weight: 0.9990 chunk 380 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 316 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 A1036 GLN ** 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 755 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.121597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079906 restraints weight = 78771.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082441 restraints weight = 45321.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084007 restraints weight = 32693.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085047 restraints weight = 27059.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085712 restraints weight = 24032.704| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 31881 Z= 0.240 Angle : 0.710 11.604 43533 Z= 0.364 Chirality : 0.047 0.207 5034 Planarity : 0.006 0.114 5514 Dihedral : 5.803 53.274 5330 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.97 % Favored : 90.72 % Rotamer: Outliers : 4.34 % Allowed : 26.14 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.13), residues: 3858 helix: 0.93 (0.19), residues: 708 sheet: -0.40 (0.17), residues: 909 loop : -2.01 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 847 TYR 0.024 0.002 TYR E 55 PHE 0.020 0.002 PHE B1121 TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00565 (31782) covalent geometry : angle 0.70210 (43281) SS BOND : bond 0.00559 ( 45) SS BOND : angle 1.33237 ( 90) hydrogen bonds : bond 0.04360 ( 1042) hydrogen bonds : angle 5.60057 ( 2802) link_NAG-ASN : bond 0.00240 ( 54) link_NAG-ASN : angle 1.67978 ( 162) *********************** 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 409 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 263 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8586 (t80) cc_final: 0.7967 (t80) REVERT: A 707 TYR cc_start: 0.8225 (t80) cc_final: 0.7910 (t80) REVERT: A 847 ARG cc_start: 0.3371 (OUTLIER) cc_final: 0.1740 (ttp-170) REVERT: A 945 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8495 (pp) REVERT: A 981 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7102 (pp) REVERT: H 2 LEU cc_start: 0.8480 (mm) cc_final: 0.8146 (mm) REVERT: H 22 CYS cc_start: 0.4922 (t) cc_final: 0.4020 (t) REVERT: H 35 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: H 38 TRP cc_start: 0.7906 (m100) cc_final: 0.7064 (m100) REVERT: H 80 LEU cc_start: 0.8747 (tp) cc_final: 0.8430 (tt) REVERT: H 101 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.8034 (t-100) REVERT: H 112 TRP cc_start: 0.8659 (p90) cc_final: 0.8212 (p90) REVERT: L 16 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.6129 (pt0) REVERT: L 87 GLU cc_start: 0.8168 (tp30) cc_final: 0.6864 (tp30) REVERT: L 107 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8120 (tppt) REVERT: B 774 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7848 (mm-40) REVERT: B 779 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8508 (tm-30) REVERT: B 873 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: B 981 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6751 (pp) REVERT: D 6 GLU cc_start: 0.6911 (pm20) cc_final: 0.6637 (pm20) REVERT: D 35 TYR cc_start: 0.6524 (t80) cc_final: 0.5932 (t80) REVERT: D 45 ARG cc_start: 0.6961 (mpp80) cc_final: 0.6729 (mpp80) REVERT: F 16 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.6147 (pt0) REVERT: C 238 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7826 (t80) REVERT: C 462 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.4916 (mttt) REVERT: C 756 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: C 945 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8245 (pp) REVERT: G 16 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6339 (pt0) outliers start: 146 outliers final: 86 residues processed: 386 average time/residue: 0.1633 time to fit residues: 105.9311 Evaluate side-chains 330 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 230 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 94 SER 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 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 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 712 ILE Chi-restraints excluded: chain A residue 760 CYS 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 945 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 965 GLN 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 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 108 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 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 704 SER Chi-restraints excluded: chain B residue 849 LEU 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 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 105 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 42 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 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 704 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 850 ILE 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 951 VAL Chi-restraints excluded: chain C residue 1009 THR 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 18 LEU Chi-restraints excluded: chain E residue 35 TYR 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 102 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 337 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 370 optimal weight: 0.0980 chunk 279 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 544 ASN 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 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 755 GLN C 856 ASN C 965 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.124033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082977 restraints weight = 79197.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085584 restraints weight = 45684.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087234 restraints weight = 32916.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088255 restraints weight = 27058.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088814 restraints weight = 24054.800| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31881 Z= 0.125 Angle : 0.648 11.526 43533 Z= 0.330 Chirality : 0.045 0.197 5034 Planarity : 0.005 0.105 5514 Dihedral : 5.401 56.148 5329 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.59 % Favored : 92.09 % Rotamer: Outliers : 3.33 % Allowed : 27.36 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.13), residues: 3858 helix: 1.08 (0.19), residues: 708 sheet: -0.34 (0.17), residues: 921 loop : -1.94 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1107 TYR 0.031 0.001 TYR B 904 PHE 0.014 0.001 PHE A 592 TRP 0.010 0.001 TRP E 38 HIS 0.004 0.001 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00283 (31782) covalent geometry : angle 0.63996 (43281) SS BOND : bond 0.00453 ( 45) SS BOND : angle 1.45253 ( 90) hydrogen bonds : bond 0.03781 ( 1042) hydrogen bonds : angle 5.31266 ( 2802) link_NAG-ASN : bond 0.00185 ( 54) link_NAG-ASN : angle 1.51059 ( 162) *********************** 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 405 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 293 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8186 (t80) cc_final: 0.7514 (t80) REVERT: A 707 TYR cc_start: 0.8085 (t80) cc_final: 0.7838 (t80) REVERT: A 847 ARG cc_start: 0.2818 (OUTLIER) cc_final: 0.1556 (ttp-170) REVERT: A 981 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7137 (pp) REVERT: A 1107 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6678 (mmm-85) REVERT: H 6 GLU cc_start: 0.6788 (pm20) cc_final: 0.6571 (pm20) REVERT: H 22 CYS cc_start: 0.4915 (t) cc_final: 0.3811 (t) REVERT: H 35 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: H 38 TRP cc_start: 0.7786 (m100) cc_final: 0.7049 (m100) REVERT: H 48 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7274 (tm-30) REVERT: H 80 LEU cc_start: 0.8658 (tp) cc_final: 0.8364 (tt) REVERT: H 112 TRP cc_start: 0.8671 (p90) cc_final: 0.8269 (p90) REVERT: L 16 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.6138 (pt0) REVERT: L 87 GLU cc_start: 0.8086 (tp30) cc_final: 0.7343 (tp30) REVERT: L 107 LYS cc_start: 0.8492 (mmmt) cc_final: 0.7951 (mmmt) REVERT: B 619 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: B 756 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6347 (m-10) REVERT: B 779 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 873 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 981 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6678 (pp) REVERT: D 35 TYR cc_start: 0.6321 (t80) cc_final: 0.5799 (t80) REVERT: D 45 ARG cc_start: 0.6839 (mpp80) cc_final: 0.6611 (mpp80) REVERT: D 55 TYR cc_start: 0.8451 (p90) cc_final: 0.8150 (p90) REVERT: F 107 LYS cc_start: 0.8360 (mmmt) cc_final: 0.8017 (mmmt) REVERT: C 462 LYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4950 (mttt) REVERT: C 945 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8213 (pp) REVERT: C 981 LEU cc_start: 0.7257 (mm) cc_final: 0.6908 (pp) REVERT: G 16 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.6288 (pt0) REVERT: G 107 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7779 (mmmt) outliers start: 112 outliers final: 66 residues processed: 377 average time/residue: 0.1572 time to fit residues: 100.1092 Evaluate side-chains 327 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 249 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 712 ILE 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 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain H residue 35 TYR 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 L residue 110 VAL Chi-restraints excluded: chain B residue 50 LEU 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 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 756 TYR 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 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 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS 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 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 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 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 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 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 271 optimal weight: 0.0060 chunk 43 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 35 optimal weight: 40.0000 chunk 236 optimal weight: 10.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** 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** ** D 118 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 C1142 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.123540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083825 restraints weight = 79604.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086274 restraints weight = 46258.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087842 restraints weight = 33411.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088816 restraints weight = 27400.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089419 restraints weight = 24333.590| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31881 Z= 0.170 Angle : 0.662 12.393 43533 Z= 0.337 Chirality : 0.046 0.208 5034 Planarity : 0.005 0.096 5514 Dihedral : 5.294 57.830 5327 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.45 % Favored : 91.24 % Rotamer: Outliers : 3.92 % Allowed : 27.48 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.13), residues: 3858 helix: 1.07 (0.20), residues: 708 sheet: -0.38 (0.17), residues: 921 loop : -1.93 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1107 TYR 0.026 0.002 TYR D 60 PHE 0.015 0.001 PHE B1121 TRP 0.034 0.001 TRP D 112 HIS 0.003 0.001 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00400 (31782) covalent geometry : angle 0.65386 (43281) SS BOND : bond 0.00466 ( 45) SS BOND : angle 1.38305 ( 90) hydrogen bonds : bond 0.03879 ( 1042) hydrogen bonds : angle 5.28597 ( 2802) link_NAG-ASN : bond 0.00150 ( 54) link_NAG-ASN : angle 1.52214 ( 162) *********************** 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 391 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 259 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8387 (t80) cc_final: 0.7750 (t80) REVERT: A 707 TYR cc_start: 0.8187 (t80) cc_final: 0.7930 (t80) REVERT: A 756 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: A 847 ARG cc_start: 0.3008 (OUTLIER) cc_final: 0.1817 (ttp-170) REVERT: A 981 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7094 (pp) REVERT: H 22 CYS cc_start: 0.4886 (t) cc_final: 0.4012 (t) REVERT: H 35 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: H 38 TRP cc_start: 0.7870 (m100) cc_final: 0.7382 (m100) REVERT: H 45 ARG cc_start: 0.6488 (mpp80) cc_final: 0.6209 (mpp80) REVERT: H 48 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7265 (tm-30) REVERT: H 101 TRP cc_start: 0.8312 (OUTLIER) cc_final: 0.7765 (t-100) REVERT: H 112 TRP cc_start: 0.8695 (p90) cc_final: 0.8243 (p90) REVERT: L 16 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6103 (pt0) REVERT: L 87 GLU cc_start: 0.8117 (tp30) cc_final: 0.7569 (tp30) REVERT: L 107 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8197 (mmmt) REVERT: B 756 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6324 (m-10) REVERT: B 774 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7616 (mm-40) REVERT: B 779 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 873 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: B 981 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6635 (pp) REVERT: D 35 TYR cc_start: 0.6348 (t80) cc_final: 0.5843 (t80) REVERT: D 45 ARG cc_start: 0.6948 (mpp80) cc_final: 0.6674 (mpp80) REVERT: F 75 LEU cc_start: 0.8339 (tp) cc_final: 0.8126 (tp) REVERT: C 238 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.7803 (t80) REVERT: C 462 LYS cc_start: 0.5300 (OUTLIER) cc_final: 0.4936 (mttt) REVERT: C 945 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8244 (pp) REVERT: C 981 LEU cc_start: 0.7266 (mm) cc_final: 0.6902 (pp) REVERT: E 112 TRP cc_start: 0.8732 (p90) cc_final: 0.8323 (p90) REVERT: G 16 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6330 (pt0) outliers start: 132 outliers final: 80 residues processed: 362 average time/residue: 0.1652 time to fit residues: 100.7757 Evaluate side-chains 338 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 245 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 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 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 538 CYS 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 712 ILE 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 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 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 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 756 TYR Chi-restraints excluded: chain B residue 841 LEU 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 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1009 THR 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 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 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 538 CYS 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 740 MET Chi-restraints excluded: chain C residue 760 CYS 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 35 TYR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 98 optimal weight: 0.6980 chunk 204 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 154 optimal weight: 0.0170 chunk 376 optimal weight: 0.0170 chunk 151 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 268 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 856 ASN A1036 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 755 GLN ** 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 ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.125812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086903 restraints weight = 79722.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090123 restraints weight = 48164.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090988 restraints weight = 31588.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.091845 restraints weight = 25298.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092029 restraints weight = 22582.353| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31881 Z= 0.113 Angle : 0.639 12.555 43533 Z= 0.323 Chirality : 0.045 0.168 5034 Planarity : 0.005 0.091 5514 Dihedral : 4.970 59.975 5327 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.47 % Favored : 92.22 % Rotamer: Outliers : 2.76 % Allowed : 28.82 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.13), residues: 3858 helix: 1.16 (0.20), residues: 711 sheet: -0.31 (0.17), residues: 924 loop : -1.86 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.013 0.001 TYR E 60 PHE 0.019 0.001 PHE B 515 TRP 0.022 0.001 TRP D 112 HIS 0.003 0.001 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00253 (31782) covalent geometry : angle 0.63251 (43281) SS BOND : bond 0.00373 ( 45) SS BOND : angle 1.16172 ( 90) hydrogen bonds : bond 0.03495 ( 1042) hydrogen bonds : angle 5.11429 ( 2802) link_NAG-ASN : bond 0.00205 ( 54) link_NAG-ASN : angle 1.43751 ( 162) *********************** 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 389 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 296 time to evaluate : 0.897 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 495 TYR cc_start: 0.0296 (OUTLIER) cc_final: -0.0644 (m-80) REVERT: A 565 PHE cc_start: 0.7846 (t80) cc_final: 0.7085 (t80) REVERT: A 619 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 847 ARG cc_start: 0.2813 (OUTLIER) cc_final: 0.1793 (ttp-170) REVERT: A 981 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7074 (pp) REVERT: A 1002 GLN cc_start: 0.8165 (mm110) cc_final: 0.7920 (tm-30) REVERT: H 22 CYS cc_start: 0.4808 (t) cc_final: 0.3812 (t) REVERT: H 35 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: H 38 TRP cc_start: 0.7708 (m100) cc_final: 0.7198 (m100) REVERT: H 45 ARG cc_start: 0.6464 (mpp80) cc_final: 0.6244 (mpp80) REVERT: H 74 ASP cc_start: 0.6543 (p0) cc_final: 0.6209 (p0) REVERT: H 101 TRP cc_start: 0.8274 (OUTLIER) cc_final: 0.7934 (t-100) REVERT: H 112 TRP cc_start: 0.8481 (p90) cc_final: 0.8203 (p90) REVERT: L 16 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6141 (pt0) REVERT: L 56 ARG cc_start: 0.8275 (ptp-170) cc_final: 0.7993 (ptt-90) REVERT: L 87 GLU cc_start: 0.8086 (tp30) cc_final: 0.7676 (tp30) REVERT: B 756 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6270 (m-10) REVERT: B 774 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7686 (mm-40) REVERT: B 779 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8412 (tm-30) REVERT: B 873 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 981 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6695 (pp) REVERT: B 1002 GLN cc_start: 0.8402 (mm110) cc_final: 0.8124 (tm-30) REVERT: D 35 TYR cc_start: 0.6090 (t80) cc_final: 0.5732 (t80) REVERT: D 45 ARG cc_start: 0.6881 (mpp80) cc_final: 0.6648 (mpp80) REVERT: D 55 TYR cc_start: 0.8375 (p90) cc_final: 0.8101 (p90) REVERT: F 75 LEU cc_start: 0.8411 (tp) cc_final: 0.8184 (tp) REVERT: F 107 LYS cc_start: 0.8368 (mmmt) cc_final: 0.8151 (mmmt) REVERT: C 294 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8142 (t70) REVERT: C 462 LYS cc_start: 0.5428 (OUTLIER) cc_final: 0.4990 (mttt) REVERT: C 619 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 756 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6518 (m-80) REVERT: C 945 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8301 (pp) REVERT: C 981 LEU cc_start: 0.7166 (mm) cc_final: 0.6844 (pp) REVERT: C 993 ILE cc_start: 0.8245 (pt) cc_final: 0.7990 (mm) REVERT: E 112 TRP cc_start: 0.8507 (p90) cc_final: 0.8276 (p90) REVERT: G 20 ILE cc_start: 0.8530 (mm) cc_final: 0.8113 (mm) REVERT: G 38 TYR cc_start: 0.7788 (m-10) cc_final: 0.7502 (m-10) REVERT: G 107 LYS cc_start: 0.8265 (mmmt) cc_final: 0.8042 (mmmt) outliers start: 93 outliers final: 62 residues processed: 366 average time/residue: 0.1692 time to fit residues: 102.6133 Evaluate side-chains 341 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 266 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 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 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 866 THR 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 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 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 756 TYR Chi-restraints excluded: chain B residue 841 LEU 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 B residue 1104 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 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 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 756 TYR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 965 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 2 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 286 optimal weight: 20.0000 chunk 266 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 343 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 367 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 856 ASN H 3 GLN ** L 39 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 755 GLN C 965 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.123760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.082898 restraints weight = 78858.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085447 restraints weight = 45523.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087021 restraints weight = 32816.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088046 restraints weight = 27047.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088682 restraints weight = 24091.933| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31881 Z= 0.146 Angle : 0.663 14.070 43533 Z= 0.333 Chirality : 0.045 0.187 5034 Planarity : 0.005 0.091 5514 Dihedral : 4.930 59.621 5327 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.93 % Favored : 91.76 % Rotamer: Outliers : 2.88 % Allowed : 28.97 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.13), residues: 3858 helix: 1.14 (0.20), residues: 711 sheet: -0.39 (0.17), residues: 957 loop : -1.90 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 17 TYR 0.027 0.001 TYR E 55 PHE 0.014 0.001 PHE B1121 TRP 0.016 0.001 TRP D 112 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00343 (31782) covalent geometry : angle 0.65675 (43281) SS BOND : bond 0.00574 ( 45) SS BOND : angle 1.21085 ( 90) hydrogen bonds : bond 0.03622 ( 1042) hydrogen bonds : angle 5.09331 ( 2802) link_NAG-ASN : bond 0.00141 ( 54) link_NAG-ASN : angle 1.46956 ( 162) *********************** 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 374 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 277 time to evaluate : 1.170 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 495 TYR cc_start: 0.0214 (OUTLIER) cc_final: -0.0761 (m-80) REVERT: A 565 PHE cc_start: 0.8178 (t80) cc_final: 0.7391 (t80) REVERT: A 619 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 756 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: A 847 ARG cc_start: 0.2753 (OUTLIER) cc_final: 0.1830 (ttp-170) REVERT: A 981 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7080 (pp) REVERT: H 22 CYS cc_start: 0.4664 (t) cc_final: 0.3837 (t) REVERT: H 35 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: H 38 TRP cc_start: 0.7765 (m100) cc_final: 0.7139 (m100) REVERT: H 45 ARG cc_start: 0.6585 (mpp80) cc_final: 0.6283 (mpp80) REVERT: H 48 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7356 (tm-30) REVERT: H 101 TRP cc_start: 0.8319 (OUTLIER) cc_final: 0.7980 (t-100) REVERT: H 112 TRP cc_start: 0.8556 (p90) cc_final: 0.8152 (p90) REVERT: L 16 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.6278 (pt0) REVERT: B 756 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6277 (m-10) REVERT: B 774 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7747 (mm-40) REVERT: B 779 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8454 (tm-30) REVERT: B 873 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: B 981 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6668 (pp) REVERT: B 1002 GLN cc_start: 0.8390 (mm110) cc_final: 0.8189 (tm-30) REVERT: D 35 TYR cc_start: 0.6354 (t80) cc_final: 0.5909 (t80) REVERT: D 45 ARG cc_start: 0.7041 (mpp80) cc_final: 0.6799 (mpp80) REVERT: F 75 LEU cc_start: 0.8364 (tp) cc_final: 0.8148 (tp) REVERT: F 107 LYS cc_start: 0.8365 (mmmt) cc_final: 0.8032 (mmmt) REVERT: C 129 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7777 (ptpt) REVERT: C 462 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.5036 (mttt) REVERT: C 619 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 756 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: C 900 MET cc_start: 0.7604 (mtp) cc_final: 0.7389 (mtp) REVERT: C 981 LEU cc_start: 0.7191 (mm) cc_final: 0.6780 (pp) REVERT: C 993 ILE cc_start: 0.8296 (pt) cc_final: 0.8084 (mt) REVERT: C 1002 GLN cc_start: 0.8241 (mm110) cc_final: 0.7891 (tm-30) REVERT: E 112 TRP cc_start: 0.8572 (p90) cc_final: 0.8304 (p90) REVERT: G 16 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.6399 (pt0) REVERT: G 20 ILE cc_start: 0.8592 (mm) cc_final: 0.8146 (mm) REVERT: G 38 TYR cc_start: 0.7833 (m-10) cc_final: 0.7530 (m-10) REVERT: G 107 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7881 (mmmt) outliers start: 97 outliers final: 69 residues processed: 352 average time/residue: 0.1678 time to fit residues: 97.8401 Evaluate side-chains 342 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 259 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 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 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS 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 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 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 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 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 756 TYR Chi-restraints excluded: chain B residue 841 LEU 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 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 129 LYS 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 965 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 79 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 162 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 856 ASN A1108 ASN ** L 39 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 755 GLN C 856 ASN C 965 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.125034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084834 restraints weight = 78609.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088738 restraints weight = 48056.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089079 restraints weight = 32599.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090144 restraints weight = 25288.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.090286 restraints weight = 22211.040| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31881 Z= 0.115 Angle : 0.660 13.403 43533 Z= 0.329 Chirality : 0.045 0.181 5034 Planarity : 0.005 0.090 5514 Dihedral : 4.764 58.254 5327 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.57 % Favored : 92.12 % Rotamer: Outliers : 2.73 % Allowed : 29.11 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.13), residues: 3858 helix: 1.16 (0.20), residues: 711 sheet: -0.38 (0.16), residues: 960 loop : -1.87 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 17 TYR 0.028 0.001 TYR E 55 PHE 0.013 0.001 PHE C 970 TRP 0.015 0.001 TRP E 38 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00262 (31782) covalent geometry : angle 0.65486 (43281) SS BOND : bond 0.00677 ( 45) SS BOND : angle 1.08156 ( 90) hydrogen bonds : bond 0.03418 ( 1042) hydrogen bonds : angle 4.99472 ( 2802) link_NAG-ASN : bond 0.00179 ( 54) link_NAG-ASN : angle 1.41390 ( 162) *********************** 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 370 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 278 time to evaluate : 0.933 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: A 495 TYR cc_start: 0.0125 (OUTLIER) cc_final: -0.1181 (m-80) REVERT: A 565 PHE cc_start: 0.7861 (t80) cc_final: 0.7224 (t80) REVERT: A 619 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 756 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: A 847 ARG cc_start: 0.2727 (OUTLIER) cc_final: 0.1789 (ttp-170) REVERT: A 981 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7060 (pp) REVERT: H 35 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: H 101 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7963 (t-100) REVERT: H 112 TRP cc_start: 0.8544 (p90) cc_final: 0.8066 (p90) REVERT: L 16 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.6290 (pt0) REVERT: B 756 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6242 (m-10) REVERT: B 779 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8436 (tm-30) REVERT: B 856 ASN cc_start: 0.7730 (t0) cc_final: 0.7200 (t0) REVERT: B 873 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: B 981 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6725 (pp) REVERT: B 1002 GLN cc_start: 0.8369 (mm110) cc_final: 0.8150 (tm-30) REVERT: D 35 TYR cc_start: 0.6252 (t80) cc_final: 0.5968 (t80) REVERT: D 38 TRP cc_start: 0.7592 (m100) cc_final: 0.6803 (m100) REVERT: D 45 ARG cc_start: 0.7054 (mpp80) cc_final: 0.6839 (mpp80) REVERT: F 56 ARG cc_start: 0.8266 (ptp-170) cc_final: 0.7975 (ptt-90) REVERT: F 75 LEU cc_start: 0.8459 (tp) cc_final: 0.8228 (tp) REVERT: F 107 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8100 (mmmt) REVERT: C 129 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7933 (ptmm) REVERT: C 462 LYS cc_start: 0.5466 (OUTLIER) cc_final: 0.5063 (mttt) REVERT: C 619 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 756 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6401 (m-10) REVERT: C 945 LEU cc_start: 0.8589 (pp) cc_final: 0.8339 (pt) REVERT: C 981 LEU cc_start: 0.7195 (mm) cc_final: 0.6847 (pp) REVERT: C 993 ILE cc_start: 0.8317 (pt) cc_final: 0.8088 (mm) REVERT: C 1002 GLN cc_start: 0.8252 (mm110) cc_final: 0.7872 (tm-30) REVERT: G 16 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6364 (pt0) REVERT: G 20 ILE cc_start: 0.8537 (mm) cc_final: 0.8096 (mm) REVERT: G 34 ASP cc_start: 0.8252 (t70) cc_final: 0.7892 (t0) REVERT: G 107 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7985 (mmmt) outliers start: 92 outliers final: 66 residues processed: 348 average time/residue: 0.1618 time to fit residues: 93.1040 Evaluate side-chains 335 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 255 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 167 THR Chi-restraints excluded: chain A residue 223 LEU 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 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 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 847 ARG 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 60 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 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 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 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU 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 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 95 THR Chi-restraints excluded: chain C residue 129 LYS 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 965 GLN 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 97 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 133 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 303 optimal weight: 0.4980 chunk 203 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 202 optimal weight: 0.1980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 856 ASN ** L 39 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 755 GLN C 965 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083131 restraints weight = 78789.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085685 restraints weight = 44821.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.087340 restraints weight = 32205.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.088355 restraints weight = 26406.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088858 restraints weight = 23478.855| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31881 Z= 0.146 Angle : 0.676 13.722 43533 Z= 0.337 Chirality : 0.045 0.184 5034 Planarity : 0.005 0.090 5514 Dihedral : 4.763 59.029 5327 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.80 % Favored : 91.89 % Rotamer: Outliers : 2.53 % Allowed : 29.32 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.13), residues: 3858 helix: 1.14 (0.20), residues: 711 sheet: -0.44 (0.16), residues: 963 loop : -1.90 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 56 TYR 0.025 0.001 TYR D 60 PHE 0.021 0.001 PHE B 392 TRP 0.040 0.001 TRP E 112 HIS 0.004 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00343 (31782) covalent geometry : angle 0.66963 (43281) SS BOND : bond 0.00539 ( 45) SS BOND : angle 1.24432 ( 90) hydrogen bonds : bond 0.03566 ( 1042) hydrogen bonds : angle 5.02699 ( 2802) link_NAG-ASN : bond 0.00135 ( 54) link_NAG-ASN : angle 1.43962 ( 162) ********************** 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 346 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 261 time to evaluate : 0.931 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 495 TYR cc_start: 0.0046 (OUTLIER) cc_final: -0.1033 (m-80) REVERT: A 565 PHE cc_start: 0.8125 (t80) cc_final: 0.7351 (t80) REVERT: A 619 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 756 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: A 981 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7070 (pp) REVERT: A 1136 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8810 (t) REVERT: H 35 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: H 101 TRP cc_start: 0.8313 (OUTLIER) cc_final: 0.8002 (t-100) REVERT: H 112 TRP cc_start: 0.8563 (p90) cc_final: 0.8121 (p90) REVERT: L 16 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6348 (pt0) REVERT: B 565 PHE cc_start: 0.8183 (t80) cc_final: 0.7898 (t80) REVERT: B 756 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6255 (m-10) REVERT: B 856 ASN cc_start: 0.7746 (t0) cc_final: 0.7235 (t0) REVERT: B 873 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: B 981 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6646 (pp) REVERT: D 35 TYR cc_start: 0.6426 (t80) cc_final: 0.6019 (t80) REVERT: D 45 ARG cc_start: 0.7129 (mpp80) cc_final: 0.6455 (mpp80) REVERT: F 56 ARG cc_start: 0.8287 (ptp-170) cc_final: 0.8011 (ptt-90) REVERT: F 75 LEU cc_start: 0.8455 (tp) cc_final: 0.8238 (tp) REVERT: F 107 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8079 (mmmt) REVERT: C 129 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8000 (ptmm) REVERT: C 462 LYS cc_start: 0.5215 (OUTLIER) cc_final: 0.4893 (mttt) REVERT: C 619 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 756 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: C 945 LEU cc_start: 0.8572 (pp) cc_final: 0.8304 (pt) REVERT: C 981 LEU cc_start: 0.7302 (mm) cc_final: 0.6934 (pp) REVERT: C 993 ILE cc_start: 0.8360 (pt) cc_final: 0.8106 (mm) REVERT: C 1002 GLN cc_start: 0.8251 (mm110) cc_final: 0.7906 (tm-30) REVERT: G 16 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6409 (pt0) REVERT: G 20 ILE cc_start: 0.8588 (mm) cc_final: 0.8150 (mm) REVERT: G 34 ASP cc_start: 0.8213 (t70) cc_final: 0.7881 (t0) REVERT: G 107 LYS cc_start: 0.8349 (mmmt) cc_final: 0.8033 (mmmt) outliers start: 85 outliers final: 66 residues processed: 327 average time/residue: 0.1687 time to fit residues: 90.7625 Evaluate side-chains 332 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 252 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 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 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS 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 712 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 847 ARG 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 A residue 1136 THR 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 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 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 869 MET Chi-restraints excluded: chain B residue 873 TYR 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 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 95 THR Chi-restraints excluded: chain C residue 129 LYS 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 965 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 132 optimal weight: 0.9990 chunk 365 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 856 ASN ** L 39 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 755 GLN C 856 ASN C 965 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.123247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082241 restraints weight = 78990.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084826 restraints weight = 44820.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086429 restraints weight = 32122.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087490 restraints weight = 26431.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088019 restraints weight = 23436.024| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31881 Z= 0.159 Angle : 0.681 13.570 43533 Z= 0.340 Chirality : 0.045 0.182 5034 Planarity : 0.005 0.089 5514 Dihedral : 4.828 59.674 5327 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.93 % Favored : 91.76 % Rotamer: Outliers : 2.79 % Allowed : 29.23 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.13), residues: 3858 helix: 1.12 (0.20), residues: 711 sheet: -0.44 (0.16), residues: 963 loop : -1.91 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 56 TYR 0.024 0.001 TYR D 60 PHE 0.013 0.001 PHE B1121 TRP 0.064 0.001 TRP E 112 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00376 (31782) covalent geometry : angle 0.67376 (43281) SS BOND : bond 0.00571 ( 45) SS BOND : angle 1.43236 ( 90) hydrogen bonds : bond 0.03662 ( 1042) hydrogen bonds : angle 5.08003 ( 2802) link_NAG-ASN : bond 0.00138 ( 54) link_NAG-ASN : angle 1.43152 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5235.28 seconds wall clock time: 91 minutes 22.33 seconds (5482.33 seconds total)