Starting phenix.real_space_refine on Wed May 28 20:28:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y4c_38915/05_2025/8y4c_38915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y4c_38915/05_2025/8y4c_38915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y4c_38915/05_2025/8y4c_38915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y4c_38915/05_2025/8y4c_38915.map" model { file = "/net/cci-nas-00/data/ceres_data/8y4c_38915/05_2025/8y4c_38915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y4c_38915/05_2025/8y4c_38915.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 19761 2.51 5 N 5115 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.47s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31050 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 813 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "B" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 813 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 813 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "B" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 16.47, per 1000 atoms: 0.53 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: 6.79 Conformation dependent library (CDL) restraints added in 3.6 seconds 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7236 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 74 sheets defined 20.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 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: 13.05 Time building geometry restraints manager: 8.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9861 1.34 - 1.47: 8131 1.47 - 1.59: 13634 1.59 - 1.72: 3 1.72 - 1.84: 153 Bond restraints: 31782 Sorted by residual: bond pdb=" CB PRO C 631 " pdb=" CG PRO C 631 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.29e+00 bond pdb=" CB PRO B 631 " pdb=" CG PRO B 631 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.87e+00 bond pdb=" CB PRO A 631 " pdb=" CG PRO A 631 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.64e+00 bond pdb=" CB PRO A 85 " pdb=" CG PRO A 85 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.25e+00 bond pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta sigma weight residual 1.469 1.447 0.022 1.28e-02 6.10e+03 3.00e+00 ... (remaining 31777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 42860 3.14 - 6.29: 378 6.29 - 9.43: 33 9.43 - 12.58: 4 12.58 - 15.72: 6 Bond angle restraints: 43281 Sorted by residual: angle pdb=" CA PRO C 631 " pdb=" N PRO C 631 " pdb=" CD PRO C 631 " ideal model delta sigma weight residual 112.00 96.28 15.72 1.40e+00 5.10e-01 1.26e+02 angle pdb=" CA PRO B 631 " pdb=" N PRO B 631 " pdb=" CD PRO B 631 " ideal model delta sigma weight residual 112.00 96.82 15.18 1.40e+00 5.10e-01 1.18e+02 angle pdb=" CA PRO A 631 " pdb=" N PRO A 631 " pdb=" CD PRO A 631 " ideal model delta sigma weight residual 112.00 97.93 14.07 1.40e+00 5.10e-01 1.01e+02 angle pdb=" CA PRO A 85 " pdb=" N PRO A 85 " pdb=" CD PRO A 85 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.41e+01 angle pdb=" CA PRO C 85 " pdb=" N PRO C 85 " pdb=" CD PRO C 85 " ideal model delta sigma weight residual 112.00 104.21 7.79 1.40e+00 5.10e-01 3.09e+01 ... (remaining 43276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 16807 17.89 - 35.78: 2098 35.78 - 53.66: 533 53.66 - 71.55: 76 71.55 - 89.44: 31 Dihedral angle restraints: 19545 sinusoidal: 8253 harmonic: 11292 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 3.56 89.44 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 3.21 -89.21 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 2.75 -88.75 1 1.00e+01 1.00e-02 9.39e+01 ... (remaining 19542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3952 0.054 - 0.109: 932 0.109 - 0.163: 128 0.163 - 0.218: 20 0.218 - 0.272: 2 Chirality restraints: 5034 Sorted by residual: chirality pdb=" CB VAL A 570 " pdb=" CA VAL A 570 " pdb=" CG1 VAL A 570 " pdb=" CG2 VAL A 570 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL B1094 " pdb=" CA VAL B1094 " pdb=" CG1 VAL B1094 " pdb=" CG2 VAL B1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE C 896 " pdb=" CA ILE C 896 " pdb=" CG1 ILE C 896 " pdb=" CG2 ILE C 896 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 5031 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 630 " 0.143 5.00e-02 4.00e+02 2.02e-01 6.51e+01 pdb=" N PRO B 631 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO B 631 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO B 631 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 630 " 0.144 5.00e-02 4.00e+02 2.01e-01 6.49e+01 pdb=" N PRO C 631 " -0.347 5.00e-02 4.00e+02 pdb=" CA PRO C 631 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO C 631 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 630 " 0.139 5.00e-02 4.00e+02 1.98e-01 6.28e+01 pdb=" N PRO A 631 " -0.342 5.00e-02 4.00e+02 pdb=" CA PRO A 631 " 0.113 5.00e-02 4.00e+02 pdb=" CD PRO A 631 " 0.090 5.00e-02 4.00e+02 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 447 2.61 - 3.18: 28083 3.18 - 3.75: 47880 3.75 - 4.33: 64045 4.33 - 4.90: 107177 Nonbonded interactions: 247632 Sorted by model distance: nonbonded pdb=" OD2 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.035 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS C 590 " model vdw 2.088 3.040 nonbonded pdb=" O CYS B 590 " pdb=" OH TYR C 837 " model vdw 2.100 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.105 3.040 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR B 837 " model vdw 2.108 3.040 ... (remaining 247627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 64.880 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 31881 Z= 0.249 Angle : 0.815 15.725 43533 Z= 0.429 Chirality : 0.048 0.272 5034 Planarity : 0.008 0.202 5514 Dihedral : 16.280 87.529 12174 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.37 % Favored : 91.32 % Rotamer: Outliers : 0.51 % Allowed : 29.17 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3858 helix: 0.57 (0.20), residues: 699 sheet: -0.46 (0.18), residues: 852 loop : -1.91 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 38 HIS 0.004 0.001 HIS L 36 PHE 0.019 0.002 PHE C 592 TYR 0.035 0.002 TYR C 904 ARG 0.008 0.001 ARG D 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 54) link_NAG-ASN : angle 1.74580 ( 162) hydrogen bonds : bond 0.21810 ( 1042) hydrogen bonds : angle 8.52065 ( 2802) SS BOND : bond 0.00428 ( 45) SS BOND : angle 1.58108 ( 90) covalent geometry : bond 0.00563 (31782) covalent geometry : angle 0.80687 (43281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 ARG cc_start: 0.6652 (mpp80) cc_final: 0.6428 (mpp80) REVERT: H 101 TRP cc_start: 0.8628 (t-100) cc_final: 0.7881 (t-100) REVERT: D 66 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8796 (ttmt) REVERT: G 34 ASP cc_start: 0.8147 (t70) cc_final: 0.7881 (m-30) outliers start: 17 outliers final: 10 residues processed: 273 average time/residue: 0.4052 time to fit residues: 182.9793 Evaluate side-chains 253 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 243 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain G residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 5.9990 chunk 293 optimal weight: 40.0000 chunk 162 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 303 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 351 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 658 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 339 HIS ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.123834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083462 restraints weight = 79823.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085995 restraints weight = 45383.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.087637 restraints weight = 32487.786| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31881 Z= 0.195 Angle : 0.698 9.127 43533 Z= 0.362 Chirality : 0.046 0.207 5034 Planarity : 0.006 0.141 5514 Dihedral : 6.382 56.166 5337 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.65 % Favored : 92.04 % Rotamer: Outliers : 3.54 % Allowed : 26.80 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3858 helix: 0.90 (0.20), residues: 705 sheet: -0.39 (0.17), residues: 921 loop : -1.98 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 38 HIS 0.003 0.001 HIS A 339 PHE 0.021 0.002 PHE C 970 TYR 0.023 0.002 TYR C 904 ARG 0.007 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 54) link_NAG-ASN : angle 1.65537 ( 162) hydrogen bonds : bond 0.04576 ( 1042) hydrogen bonds : angle 6.08885 ( 2802) SS BOND : bond 0.00527 ( 45) SS BOND : angle 1.24680 ( 90) covalent geometry : bond 0.00449 (31782) covalent geometry : angle 0.68993 (43281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 275 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 ARG cc_start: 0.3267 (OUTLIER) cc_final: 0.1786 (ttp-170) REVERT: H 6 GLU cc_start: 0.6942 (pm20) cc_final: 0.6648 (pm20) REVERT: H 22 CYS cc_start: 0.4873 (t) cc_final: 0.3994 (t) REVERT: H 35 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: H 38 TRP cc_start: 0.7926 (m100) cc_final: 0.7603 (m100) REVERT: H 48 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7088 (tm-30) REVERT: H 106 LEU cc_start: 0.8827 (mm) cc_final: 0.8579 (tp) REVERT: L 107 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7894 (mmmt) REVERT: B 495 TYR cc_start: -0.0622 (OUTLIER) cc_final: -0.2129 (m-80) REVERT: B 565 PHE cc_start: 0.8330 (t80) cc_final: 0.8000 (t80) REVERT: B 779 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8573 (tm-30) REVERT: D 35 TYR cc_start: 0.6095 (t80) cc_final: 0.5596 (t80) REVERT: D 38 TRP cc_start: 0.7834 (m100) cc_final: 0.6955 (m100) REVERT: D 45 ARG cc_start: 0.6770 (mpp80) cc_final: 0.6492 (mpp80) REVERT: F 17 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: F 47 LYS cc_start: 0.8091 (tttt) cc_final: 0.7865 (tttp) REVERT: C 462 LYS cc_start: 0.5097 (OUTLIER) cc_final: 0.4743 (mttt) REVERT: C 945 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8117 (pp) outliers start: 119 outliers final: 66 residues processed: 365 average time/residue: 0.4159 time to fit residues: 251.1126 Evaluate side-chains 303 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 232 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 34 ASP Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 383 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 344 optimal weight: 0.0970 chunk 254 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 168 optimal weight: 30.0000 chunk 67 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 348 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- 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 A1083 HIS H 5 GLN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 856 ASN C 965 GLN C1083 HIS ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.121977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080501 restraints weight = 78964.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083059 restraints weight = 45187.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084696 restraints weight = 32456.631| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31881 Z= 0.214 Angle : 0.692 13.317 43533 Z= 0.356 Chirality : 0.047 0.198 5034 Planarity : 0.006 0.118 5514 Dihedral : 6.007 53.489 5330 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.27 % Favored : 91.42 % Rotamer: Outliers : 4.87 % Allowed : 25.67 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 3858 helix: 0.91 (0.19), residues: 705 sheet: -0.35 (0.17), residues: 918 loop : -2.05 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.018 0.002 PHE C 970 TYR 0.023 0.002 TYR B 904 ARG 0.006 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 54) link_NAG-ASN : angle 1.65080 ( 162) hydrogen bonds : bond 0.04475 ( 1042) hydrogen bonds : angle 5.69851 ( 2802) SS BOND : bond 0.00453 ( 45) SS BOND : angle 1.18779 ( 90) covalent geometry : bond 0.00498 (31782) covalent geometry : angle 0.68487 (43281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 274 time to evaluate : 3.057 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 707 TYR cc_start: 0.8165 (t80) cc_final: 0.7856 (t80) REVERT: A 847 ARG cc_start: 0.3416 (OUTLIER) cc_final: 0.1707 (ttp-170) REVERT: H 22 CYS cc_start: 0.4937 (t) cc_final: 0.4033 (t) REVERT: H 35 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: H 38 TRP cc_start: 0.7839 (m100) cc_final: 0.7412 (m100) REVERT: H 48 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7147 (tm-30) REVERT: H 101 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.8128 (t-100) REVERT: H 112 TRP cc_start: 0.8639 (p90) cc_final: 0.8211 (p90) REVERT: L 16 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6175 (pt0) REVERT: L 87 GLU cc_start: 0.8209 (tp30) cc_final: 0.6981 (tp30) REVERT: L 107 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8090 (tppt) REVERT: B 774 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7858 (mm-40) REVERT: B 779 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8541 (tm-30) REVERT: B 847 ARG cc_start: 0.2990 (OUTLIER) cc_final: 0.1845 (ttp-170) REVERT: B 873 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: D 35 TYR cc_start: 0.6417 (t80) cc_final: 0.5795 (t80) REVERT: D 45 ARG cc_start: 0.6851 (mpp80) cc_final: 0.6387 (mpp80) REVERT: F 16 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.6080 (pt0) REVERT: F 17 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7658 (mmm-85) REVERT: F 47 LYS cc_start: 0.8021 (tttt) cc_final: 0.7812 (tttp) REVERT: C 238 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7823 (t80) REVERT: C 462 LYS cc_start: 0.5301 (OUTLIER) cc_final: 0.4966 (mttt) REVERT: C 756 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6513 (m-10) REVERT: C 945 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8265 (pp) REVERT: E 6 GLU cc_start: 0.5503 (pm20) cc_final: 0.5252 (pm20) REVERT: E 13 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8486 (mmmt) REVERT: E 118 GLN cc_start: 0.6960 (pm20) cc_final: 0.6391 (pm20) REVERT: G 16 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6431 (pt0) REVERT: G 39 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7746 (tm-30) outliers start: 164 outliers final: 88 residues processed: 415 average time/residue: 0.3593 time to fit residues: 249.9536 Evaluate side-chains 340 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 240 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 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 568 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 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 923 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain 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 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 760 CYS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1009 THR 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 53 ASN 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 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 847 ARG Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 915 VAL 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 1034 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 34 ASP Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 13 optimal weight: 3.9990 chunk 352 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 167 optimal weight: 40.0000 chunk 205 optimal weight: 0.9990 chunk 376 optimal weight: 0.0040 chunk 290 optimal weight: 10.0000 chunk 170 optimal weight: 50.0000 chunk 349 optimal weight: 6.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 965 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.124219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084973 restraints weight = 79605.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088320 restraints weight = 48397.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089059 restraints weight = 31259.771| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31881 Z= 0.139 Angle : 0.644 11.345 43533 Z= 0.331 Chirality : 0.045 0.160 5034 Planarity : 0.005 0.111 5514 Dihedral : 5.582 56.115 5329 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.85 % Favored : 91.84 % Rotamer: Outliers : 3.36 % Allowed : 27.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 3858 helix: 1.06 (0.20), residues: 708 sheet: -0.34 (0.17), residues: 915 loop : -1.98 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 38 HIS 0.004 0.001 HIS L 36 PHE 0.015 0.001 PHE A 592 TYR 0.025 0.001 TYR E 55 ARG 0.006 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 54) link_NAG-ASN : angle 1.54633 ( 162) hydrogen bonds : bond 0.03863 ( 1042) hydrogen bonds : angle 5.43410 ( 2802) SS BOND : bond 0.00523 ( 45) SS BOND : angle 1.09866 ( 90) covalent geometry : bond 0.00321 (31782) covalent geometry : angle 0.63734 (43281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 285 time to evaluate : 3.525 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 565 PHE cc_start: 0.8309 (t80) cc_final: 0.7707 (t80) REVERT: A 707 TYR cc_start: 0.8087 (t80) cc_final: 0.7812 (t80) REVERT: A 847 ARG cc_start: 0.3055 (OUTLIER) cc_final: 0.1688 (ttp-170) REVERT: A 981 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7220 (pp) REVERT: A 1107 ARG cc_start: 0.7481 (mmm-85) cc_final: 0.7056 (mmm-85) REVERT: H 2 LEU cc_start: 0.8587 (mm) cc_final: 0.8269 (mm) REVERT: H 22 CYS cc_start: 0.5088 (t) cc_final: 0.3930 (t) REVERT: H 35 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: H 38 TRP cc_start: 0.7776 (m100) cc_final: 0.6922 (m100) REVERT: H 80 LEU cc_start: 0.8718 (tp) cc_final: 0.8405 (tt) REVERT: H 112 TRP cc_start: 0.8581 (p90) cc_final: 0.8223 (p90) REVERT: L 16 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6178 (pt0) REVERT: L 87 GLU cc_start: 0.8127 (tp30) cc_final: 0.7311 (tp30) REVERT: L 107 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7873 (mmmt) REVERT: B 565 PHE cc_start: 0.8220 (t80) cc_final: 0.7854 (t80) REVERT: B 774 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7873 (mm-40) REVERT: B 779 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8461 (tm-30) REVERT: B 847 ARG cc_start: 0.2554 (OUTLIER) cc_final: 0.1532 (ttp-170) REVERT: B 873 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: B 981 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6783 (pp) REVERT: D 6 GLU cc_start: 0.6716 (pm20) cc_final: 0.6502 (pm20) REVERT: D 35 TYR cc_start: 0.6302 (t80) cc_final: 0.5821 (t80) REVERT: D 45 ARG cc_start: 0.6802 (mpp80) cc_final: 0.6600 (mpp80) REVERT: C 238 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.7766 (t80) REVERT: C 462 LYS cc_start: 0.5332 (OUTLIER) cc_final: 0.4885 (mttt) REVERT: C 945 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8249 (pp) REVERT: E 118 GLN cc_start: 0.6889 (pm20) cc_final: 0.6619 (pm20) REVERT: G 16 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6329 (pt0) REVERT: G 107 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7950 (mmmt) outliers start: 113 outliers final: 64 residues processed: 373 average time/residue: 0.3995 time to fit residues: 249.0978 Evaluate side-chains 319 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 244 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 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 568 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain D residue 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 F residue 101 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 CYS 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 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 760 CYS Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain G residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 310 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 357 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 263 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 339 HIS C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.123236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083096 restraints weight = 79841.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085606 restraints weight = 45367.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087251 restraints weight = 32359.409| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31881 Z= 0.177 Angle : 0.667 11.803 43533 Z= 0.341 Chirality : 0.046 0.192 5034 Planarity : 0.005 0.103 5514 Dihedral : 5.459 58.076 5327 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.40 % Favored : 91.29 % Rotamer: Outliers : 4.40 % Allowed : 26.80 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3858 helix: 1.07 (0.20), residues: 708 sheet: -0.40 (0.17), residues: 921 loop : -1.98 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 112 HIS 0.005 0.001 HIS F 36 PHE 0.015 0.001 PHE B1121 TYR 0.026 0.001 TYR H 60 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 54) link_NAG-ASN : angle 1.58060 ( 162) hydrogen bonds : bond 0.03945 ( 1042) hydrogen bonds : angle 5.39312 ( 2802) SS BOND : bond 0.00604 ( 45) SS BOND : angle 1.35603 ( 90) covalent geometry : bond 0.00416 (31782) covalent geometry : angle 0.65883 (43281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 267 time to evaluate : 3.145 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: 0.8407 (t80) cc_final: 0.7854 (t80) REVERT: A 707 TYR cc_start: 0.8218 (t80) cc_final: 0.7971 (t80) REVERT: A 847 ARG cc_start: 0.2973 (OUTLIER) cc_final: 0.1859 (ttp-170) REVERT: A 981 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7162 (pp) REVERT: H 22 CYS cc_start: 0.5000 (t) cc_final: 0.3967 (t) REVERT: H 35 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: H 38 TRP cc_start: 0.7908 (m100) cc_final: 0.7073 (m100) REVERT: H 45 ARG cc_start: 0.6462 (mpp80) cc_final: 0.6187 (mpp80) REVERT: H 48 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7306 (tm-30) REVERT: H 80 LEU cc_start: 0.8671 (tp) cc_final: 0.8384 (tt) REVERT: H 101 TRP cc_start: 0.8339 (OUTLIER) cc_final: 0.7773 (t-100) REVERT: H 112 TRP cc_start: 0.8627 (p90) cc_final: 0.8241 (p90) REVERT: L 16 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6163 (pt0) REVERT: L 87 GLU cc_start: 0.8142 (tp30) cc_final: 0.7593 (tp30) REVERT: L 107 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8170 (mmmt) REVERT: B 619 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: B 779 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8479 (tm-30) REVERT: B 847 ARG cc_start: 0.2547 (OUTLIER) cc_final: 0.1568 (ttt-90) REVERT: B 873 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: B 981 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6735 (pp) REVERT: D 6 GLU cc_start: 0.6643 (pm20) cc_final: 0.6425 (pm20) REVERT: D 35 TYR cc_start: 0.6455 (t80) cc_final: 0.5862 (t80) REVERT: D 45 ARG cc_start: 0.6909 (mpp80) cc_final: 0.6615 (mpp80) REVERT: F 16 GLN cc_start: 0.6519 (OUTLIER) cc_final: 0.6255 (pt0) REVERT: F 107 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7986 (mmmt) REVERT: C 238 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7765 (t80) REVERT: C 462 LYS cc_start: 0.5291 (OUTLIER) cc_final: 0.4940 (mttt) REVERT: C 756 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: C 945 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8295 (pp) REVERT: C 981 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6982 (pp) REVERT: G 16 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6365 (pt0) outliers start: 148 outliers final: 91 residues processed: 391 average time/residue: 0.3718 time to fit residues: 244.9628 Evaluate side-chains 351 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 244 time to evaluate : 3.110 ------------------------------------------------------------------------------- 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 108 THR Chi-restraints excluded: chain A residue 130 VAL 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 294 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 841 LEU 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 1009 THR Chi-restraints excluded: chain A residue 1104 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 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 42 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 849 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 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 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 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 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 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 101 VAL Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 53 optimal weight: 0.0980 chunk 30 optimal weight: 20.0000 chunk 85 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 329 optimal weight: 0.8980 chunk 377 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.124188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083485 restraints weight = 78916.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086048 restraints weight = 45066.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087669 restraints weight = 32342.258| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31881 Z= 0.121 Angle : 0.637 12.470 43533 Z= 0.325 Chirality : 0.045 0.182 5034 Planarity : 0.005 0.095 5514 Dihedral : 5.151 59.477 5327 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.62 % Favored : 92.07 % Rotamer: Outliers : 3.48 % Allowed : 28.07 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3858 helix: 1.16 (0.20), residues: 711 sheet: -0.36 (0.17), residues: 936 loop : -1.90 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 112 HIS 0.003 0.001 HIS F 36 PHE 0.015 0.001 PHE C 374 TYR 0.029 0.001 TYR E 55 ARG 0.016 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 54) link_NAG-ASN : angle 1.49924 ( 162) hydrogen bonds : bond 0.03581 ( 1042) hydrogen bonds : angle 5.17628 ( 2802) SS BOND : bond 0.00481 ( 45) SS BOND : angle 1.12704 ( 90) covalent geometry : bond 0.00278 (31782) covalent geometry : angle 0.62966 (43281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 296 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8018 (t80) cc_final: 0.7370 (t80) REVERT: A 847 ARG cc_start: 0.3097 (OUTLIER) cc_final: 0.1986 (ttp-170) REVERT: A 981 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7120 (pp) REVERT: H 22 CYS cc_start: 0.4895 (t) cc_final: 0.3719 (t) REVERT: H 35 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: H 38 TRP cc_start: 0.7778 (m100) cc_final: 0.7113 (m100) REVERT: H 45 ARG cc_start: 0.6424 (mpp80) cc_final: 0.6124 (mpp80) REVERT: H 48 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7198 (tm-30) REVERT: H 80 LEU cc_start: 0.8635 (tp) cc_final: 0.8340 (tt) REVERT: H 101 TRP cc_start: 0.8310 (OUTLIER) cc_final: 0.7786 (t-100) REVERT: H 112 TRP cc_start: 0.8484 (p90) cc_final: 0.8202 (p90) REVERT: L 87 GLU cc_start: 0.8091 (tp30) cc_final: 0.7588 (tp30) REVERT: L 107 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8275 (mmmt) REVERT: B 779 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 847 ARG cc_start: 0.2502 (OUTLIER) cc_final: 0.1891 (ttt-90) REVERT: B 873 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: B 981 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6669 (pp) REVERT: D 35 TYR cc_start: 0.6331 (t80) cc_final: 0.5818 (t80) REVERT: D 45 ARG cc_start: 0.6923 (mpp80) cc_final: 0.6673 (mpp80) REVERT: D 112 TRP cc_start: 0.8508 (p90) cc_final: 0.8286 (p90) REVERT: F 75 LEU cc_start: 0.8350 (tp) cc_final: 0.8137 (tp) REVERT: F 107 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8168 (mmmt) REVERT: C 462 LYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4981 (mttt) REVERT: C 756 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: C 856 ASN cc_start: 0.7451 (m-40) cc_final: 0.7235 (m110) REVERT: C 945 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8305 (pp) REVERT: C 981 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6960 (pp) REVERT: E 112 TRP cc_start: 0.8586 (p90) cc_final: 0.8276 (p90) REVERT: G 38 TYR cc_start: 0.7837 (m-10) cc_final: 0.7606 (m-10) REVERT: G 87 GLU cc_start: 0.8608 (tp30) cc_final: 0.8363 (tp30) REVERT: G 107 LYS cc_start: 0.8265 (mmmt) cc_final: 0.8002 (mmmt) outliers start: 117 outliers final: 71 residues processed: 386 average time/residue: 0.4257 time to fit residues: 273.8808 Evaluate side-chains 339 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 257 time to evaluate : 3.354 ------------------------------------------------------------------------------- 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 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 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 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 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 752 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 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 590 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR 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 6 optimal weight: 0.0370 chunk 325 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 297 optimal weight: 8.9990 chunk 310 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.124883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085034 restraints weight = 79372.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087643 restraints weight = 44565.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089295 restraints weight = 31612.574| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31881 Z= 0.130 Angle : 0.651 12.752 43533 Z= 0.329 Chirality : 0.045 0.183 5034 Planarity : 0.005 0.089 5514 Dihedral : 5.039 58.469 5327 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.06 % Favored : 91.63 % Rotamer: Outliers : 3.39 % Allowed : 28.16 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3858 helix: 1.16 (0.20), residues: 711 sheet: -0.31 (0.17), residues: 936 loop : -1.86 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 112 HIS 0.003 0.000 HIS B1048 PHE 0.031 0.001 PHE A 392 TYR 0.026 0.001 TYR D 55 ARG 0.015 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 54) link_NAG-ASN : angle 1.48766 ( 162) hydrogen bonds : bond 0.03566 ( 1042) hydrogen bonds : angle 5.12300 ( 2802) SS BOND : bond 0.00541 ( 45) SS BOND : angle 1.39810 ( 90) covalent geometry : bond 0.00303 (31782) covalent geometry : angle 0.64380 (43281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 282 time to evaluate : 3.344 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: 0.0224 (OUTLIER) cc_final: -0.0514 (m-80) REVERT: A 565 PHE cc_start: 0.8081 (t80) cc_final: 0.7425 (t80) REVERT: A 756 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: A 847 ARG cc_start: 0.3174 (OUTLIER) cc_final: 0.2157 (ttp-170) REVERT: A 981 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7101 (pp) REVERT: A 1136 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8778 (t) REVERT: H 22 CYS cc_start: 0.4692 (t) cc_final: 0.3737 (t) REVERT: H 35 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: H 38 TRP cc_start: 0.7790 (m100) cc_final: 0.7190 (m100) REVERT: H 45 ARG cc_start: 0.6583 (mpp80) cc_final: 0.6313 (mpp80) REVERT: H 48 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7153 (tm-30) REVERT: H 101 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.7927 (t-100) REVERT: H 112 TRP cc_start: 0.8490 (p90) cc_final: 0.8173 (p90) REVERT: L 16 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6270 (pt0) REVERT: L 56 ARG cc_start: 0.8253 (ptp-170) cc_final: 0.8044 (ptt180) REVERT: L 87 GLU cc_start: 0.8065 (tp30) cc_final: 0.7624 (tp30) REVERT: B 756 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6331 (m-10) REVERT: B 779 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8430 (tm-30) REVERT: B 856 ASN cc_start: 0.7563 (t0) cc_final: 0.7206 (t0) REVERT: B 873 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: B 981 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6646 (pp) REVERT: B 1002 GLN cc_start: 0.8402 (mm110) cc_final: 0.8198 (tm-30) REVERT: D 35 TYR cc_start: 0.6237 (t80) cc_final: 0.5850 (t80) REVERT: D 45 ARG cc_start: 0.6935 (mpp80) cc_final: 0.6684 (mpp80) REVERT: D 55 TYR cc_start: 0.8351 (p90) cc_final: 0.8083 (p90) REVERT: D 112 TRP cc_start: 0.8560 (p90) cc_final: 0.8327 (p90) REVERT: F 75 LEU cc_start: 0.8390 (tp) cc_final: 0.8176 (tp) REVERT: F 107 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8159 (mmmt) REVERT: C 462 LYS cc_start: 0.5240 (OUTLIER) cc_final: 0.4922 (mttt) REVERT: C 756 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6298 (m-10) REVERT: C 856 ASN cc_start: 0.7470 (m-40) cc_final: 0.7257 (m110) REVERT: C 945 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8324 (pp) REVERT: C 981 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6960 (pp) REVERT: E 112 TRP cc_start: 0.8569 (p90) cc_final: 0.8326 (p90) REVERT: G 16 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6424 (pt0) REVERT: G 20 ILE cc_start: 0.8575 (mm) cc_final: 0.8144 (mm) REVERT: G 38 TYR cc_start: 0.7855 (m-10) cc_final: 0.7581 (m-10) outliers start: 114 outliers final: 78 residues processed: 369 average time/residue: 0.3866 time to fit residues: 236.4423 Evaluate side-chains 354 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 260 time to evaluate : 3.135 ------------------------------------------------------------------------------- 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 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 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 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 B residue 42 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 380 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 346 optimal weight: 0.4980 chunk 149 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 196 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1142 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 965 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.123875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083820 restraints weight = 79950.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086361 restraints weight = 45318.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087993 restraints weight = 32309.528| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31881 Z= 0.160 Angle : 0.667 13.047 43533 Z= 0.336 Chirality : 0.045 0.181 5034 Planarity : 0.005 0.090 5514 Dihedral : 5.019 57.396 5327 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.93 % Favored : 91.76 % Rotamer: Outliers : 3.59 % Allowed : 28.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3858 helix: 1.12 (0.20), residues: 711 sheet: -0.38 (0.17), residues: 936 loop : -1.85 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 38 HIS 0.002 0.001 HIS B1048 PHE 0.017 0.001 PHE A 392 TYR 0.028 0.001 TYR E 55 ARG 0.014 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 54) link_NAG-ASN : angle 1.50471 ( 162) hydrogen bonds : bond 0.03694 ( 1042) hydrogen bonds : angle 5.15200 ( 2802) SS BOND : bond 0.00441 ( 45) SS BOND : angle 1.19365 ( 90) covalent geometry : bond 0.00378 (31782) covalent geometry : angle 0.66041 (43281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 264 time to evaluate : 3.461 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: 0.0233 (OUTLIER) cc_final: -0.0741 (m-80) REVERT: A 565 PHE cc_start: 0.8234 (t80) cc_final: 0.7621 (t80) REVERT: A 756 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6679 (m-10) REVERT: A 847 ARG cc_start: 0.3350 (OUTLIER) cc_final: 0.2342 (ttp-170) REVERT: A 981 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7048 (pp) REVERT: A 1107 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6611 (mmm-85) REVERT: A 1136 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8821 (t) REVERT: H 35 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: H 45 ARG cc_start: 0.6623 (mpp80) cc_final: 0.6305 (mpp80) REVERT: H 101 TRP cc_start: 0.8322 (OUTLIER) cc_final: 0.7724 (t-100) REVERT: H 112 TRP cc_start: 0.8561 (p90) cc_final: 0.8201 (p90) REVERT: L 16 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6178 (pt0) REVERT: L 17 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7676 (mmm-85) REVERT: L 56 ARG cc_start: 0.8280 (ptp-170) cc_final: 0.8076 (ptt180) REVERT: B 756 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6343 (m-10) REVERT: B 779 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8455 (tm-30) REVERT: B 873 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: B 981 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6648 (pp) REVERT: D 45 ARG cc_start: 0.7075 (mpp80) cc_final: 0.6807 (mpp80) REVERT: D 55 TYR cc_start: 0.8382 (p90) cc_final: 0.8123 (p90) REVERT: C 462 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.5039 (mttt) REVERT: C 756 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6288 (m-10) REVERT: C 856 ASN cc_start: 0.7548 (m-40) cc_final: 0.7320 (m110) REVERT: C 965 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: C 981 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7005 (pp) REVERT: E 112 TRP cc_start: 0.8655 (p90) cc_final: 0.8343 (p90) REVERT: G 16 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6511 (pt0) REVERT: G 38 TYR cc_start: 0.7874 (m-10) cc_final: 0.7602 (m-10) outliers start: 121 outliers final: 80 residues processed: 361 average time/residue: 0.3901 time to fit residues: 231.9094 Evaluate side-chains 343 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 246 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 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 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 A residue 1107 ARG 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 H residue 121 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 35 TYR 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 71 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 344 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 318 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 367 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 965 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.123402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084323 restraints weight = 80072.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087380 restraints weight = 48970.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088142 restraints weight = 32630.884| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2354 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 : 0.685 12.630 43533 Z= 0.344 Chirality : 0.046 0.178 5034 Planarity : 0.005 0.092 5514 Dihedral : 5.052 59.793 5327 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.29 % Favored : 91.39 % Rotamer: Outliers : 3.21 % Allowed : 28.76 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3858 helix: 1.13 (0.20), residues: 711 sheet: -0.48 (0.16), residues: 969 loop : -1.88 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 38 HIS 0.002 0.001 HIS A1048 PHE 0.014 0.001 PHE A 392 TYR 0.042 0.002 TYR B 904 ARG 0.017 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 54) link_NAG-ASN : angle 1.50013 ( 162) hydrogen bonds : bond 0.03766 ( 1042) hydrogen bonds : angle 5.14340 ( 2802) SS BOND : bond 0.00443 ( 45) SS BOND : angle 1.22125 ( 90) covalent geometry : bond 0.00399 (31782) covalent geometry : angle 0.67890 (43281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 273 time to evaluate : 3.255 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: A 495 TYR cc_start: 0.0262 (OUTLIER) cc_final: -0.1018 (m-80) REVERT: A 565 PHE cc_start: 0.8238 (t80) cc_final: 0.7622 (t80) REVERT: A 756 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: A 847 ARG cc_start: 0.3389 (OUTLIER) cc_final: 0.2378 (ttp-170) REVERT: A 981 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7021 (pp) REVERT: A 1136 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8822 (t) REVERT: H 35 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: H 45 ARG cc_start: 0.6642 (mpp80) cc_final: 0.6222 (mpp80) REVERT: H 48 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7283 (tm-30) REVERT: H 101 TRP cc_start: 0.8334 (OUTLIER) cc_final: 0.7743 (t-100) REVERT: H 112 TRP cc_start: 0.8560 (p90) cc_final: 0.8133 (p90) REVERT: L 16 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6200 (pt0) REVERT: L 17 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7664 (mmm-85) REVERT: L 32 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8695 (tpp80) REVERT: B 756 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6377 (m-10) REVERT: B 779 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 873 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: B 981 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6724 (pp) REVERT: D 45 ARG cc_start: 0.7068 (mpp80) cc_final: 0.6375 (mpp80) REVERT: D 55 TYR cc_start: 0.8436 (p90) cc_final: 0.8150 (p90) REVERT: C 462 LYS cc_start: 0.5302 (OUTLIER) cc_final: 0.4922 (mttt) REVERT: C 756 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: C 856 ASN cc_start: 0.7629 (m-40) cc_final: 0.7427 (m110) REVERT: C 981 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6926 (pp) REVERT: C 1002 GLN cc_start: 0.8193 (mm110) cc_final: 0.7947 (tm-30) REVERT: E 45 ARG cc_start: 0.6091 (mmp80) cc_final: 0.5874 (mmp80) REVERT: E 112 TRP cc_start: 0.8692 (p90) cc_final: 0.8362 (p90) REVERT: G 16 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6557 (pt0) REVERT: G 20 ILE cc_start: 0.8617 (mm) cc_final: 0.8187 (mm) REVERT: G 38 TYR cc_start: 0.7867 (m-10) cc_final: 0.7584 (m-10) outliers start: 108 outliers final: 85 residues processed: 359 average time/residue: 0.4030 time to fit residues: 239.5517 Evaluate side-chains 354 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 254 time to evaluate : 3.564 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 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 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 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 42 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 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 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 102 optimal weight: 0.5980 chunk 349 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.120639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079454 restraints weight = 79504.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.083057 restraints weight = 50588.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083463 restraints weight = 32280.780| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 31881 Z= 0.270 Angle : 0.748 12.647 43533 Z= 0.379 Chirality : 0.048 0.194 5034 Planarity : 0.005 0.099 5514 Dihedral : 5.385 58.144 5327 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.28 % Favored : 90.41 % Rotamer: Outliers : 3.30 % Allowed : 28.73 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3858 helix: 1.03 (0.20), residues: 711 sheet: -0.60 (0.17), residues: 897 loop : -1.94 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.003 0.001 HIS C 519 PHE 0.021 0.002 PHE C1121 TYR 0.038 0.002 TYR D 60 ARG 0.014 0.001 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 54) link_NAG-ASN : angle 1.62134 ( 162) hydrogen bonds : bond 0.04220 ( 1042) hydrogen bonds : angle 5.32400 ( 2802) SS BOND : bond 0.00701 ( 45) SS BOND : angle 1.62145 ( 90) covalent geometry : bond 0.00632 (31782) covalent geometry : angle 0.74014 (43281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 245 time to evaluate : 3.290 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: 0.0207 (OUTLIER) cc_final: -0.1232 (m-80) REVERT: A 565 PHE cc_start: 0.8480 (t80) cc_final: 0.7907 (t80) REVERT: A 756 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: A 847 ARG cc_start: 0.3521 (OUTLIER) cc_final: 0.2425 (ttp-170) REVERT: A 856 ASN cc_start: 0.7665 (m-40) cc_final: 0.7435 (m110) REVERT: A 1136 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8868 (t) REVERT: H 35 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: H 45 ARG cc_start: 0.6744 (mpp80) cc_final: 0.6137 (mpp80) REVERT: H 48 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7247 (tm-30) REVERT: H 101 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7754 (t-100) REVERT: H 112 TRP cc_start: 0.8709 (p90) cc_final: 0.8204 (p90) REVERT: L 16 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6162 (pt0) REVERT: L 17 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7692 (mmm-85) REVERT: L 32 ARG cc_start: 0.9000 (tpp80) cc_final: 0.8764 (tpp80) REVERT: B 198 ASP cc_start: 0.7865 (p0) cc_final: 0.7590 (p0) REVERT: B 756 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6490 (m-10) REVERT: B 779 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8478 (tm-30) REVERT: B 847 ARG cc_start: 0.2871 (OUTLIER) cc_final: 0.2130 (ttp-170) REVERT: B 873 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: D 55 TYR cc_start: 0.8442 (p90) cc_final: 0.8137 (p90) REVERT: C 238 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7836 (t80) REVERT: C 462 LYS cc_start: 0.5319 (OUTLIER) cc_final: 0.4935 (mttt) REVERT: C 756 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6273 (m-10) REVERT: C 847 ARG cc_start: 0.2932 (OUTLIER) cc_final: 0.2691 (ttp-110) REVERT: C 856 ASN cc_start: 0.7644 (m-40) cc_final: 0.7431 (m110) REVERT: C 900 MET cc_start: 0.7652 (mtp) cc_final: 0.7414 (mtp) REVERT: E 112 TRP cc_start: 0.8793 (p90) cc_final: 0.8336 (p90) REVERT: G 16 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6714 (pt0) REVERT: G 20 ILE cc_start: 0.8590 (mm) cc_final: 0.8190 (mm) REVERT: G 38 TYR cc_start: 0.7897 (m-10) cc_final: 0.7652 (m-10) outliers start: 111 outliers final: 84 residues processed: 337 average time/residue: 0.4037 time to fit residues: 223.5143 Evaluate side-chains 331 residues out of total 3375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 232 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 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 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain 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 42 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 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 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 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 586 ASP Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 129 optimal weight: 10.0000 chunk 262 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 188 optimal weight: 0.0980 chunk 138 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.122966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.084013 restraints weight = 79778.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087056 restraints weight = 48719.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087832 restraints weight = 32324.883| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31881 Z= 0.162 Angle : 0.691 13.088 43533 Z= 0.347 Chirality : 0.046 0.190 5034 Planarity : 0.005 0.099 5514 Dihedral : 5.192 55.165 5327 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.11 % Favored : 91.58 % Rotamer: Outliers : 3.12 % Allowed : 28.97 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3858 helix: 1.11 (0.20), residues: 711 sheet: -0.54 (0.17), residues: 957 loop : -1.89 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 112 HIS 0.003 0.001 HIS A1048 PHE 0.013 0.001 PHE B 392 TYR 0.024 0.001 TYR D 60 ARG 0.007 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 54) link_NAG-ASN : angle 1.51541 ( 162) hydrogen bonds : bond 0.03762 ( 1042) hydrogen bonds : angle 5.19731 ( 2802) SS BOND : bond 0.00442 ( 45) SS BOND : angle 1.22320 ( 90) covalent geometry : bond 0.00384 (31782) covalent geometry : angle 0.68469 (43281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10027.17 seconds wall clock time: 176 minutes 46.39 seconds (10606.39 seconds total)