Starting phenix.real_space_refine on Thu Nov 20 01:31:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y4a_38914/11_2025/8y4a_38914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y4a_38914/11_2025/8y4a_38914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y4a_38914/11_2025/8y4a_38914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y4a_38914/11_2025/8y4a_38914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y4a_38914/11_2025/8y4a_38914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y4a_38914/11_2025/8y4a_38914.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.079 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 128 5.16 5 C 18740 2.51 5 N 4811 2.21 5 O 5737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29416 Number of models: 1 Model: "" Number of chains: 24 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: "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: "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: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "D" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 7.00, per 1000 atoms: 0.24 Number of scatterers: 29416 At special positions: 0 Unit cell: (147.66, 153.01, 192.6, 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 128 16.00 O 5737 8.00 N 4811 7.00 C 18740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 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 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS 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 A 131 " - pdb=" SG CYS A 166 " 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " 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=2.03 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 354 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 245 " " NAG A1314 " - " ASN A 282 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 245 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B 354 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 122 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 245 " " NAG C1312 " - " ASN C 603 " " NAG F 1 " - " ASN B 801 " " NAG G 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 165 " " NAG K 2 " - " ASN C 354 " " NAG M 1 " - " ASN C 282 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN A 717 " " NAG T 1 " - " ASN A1098 " " NAG U 1 " - " ASN A1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6790 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 61 sheets defined 21.7% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.812A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.915A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.653A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 627 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.598A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 840 through 844 removed outlier: 3.557A pdb=" N ASP B 843 " --> pdb=" O CYS B 840 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 840 through 844' Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.523A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) 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: 4.347A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.859A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.500A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.767A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.812A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.550A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.917A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.521A pdb=" N VAL C 407 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.554A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.766A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.246A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.336A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.500A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.962A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.632A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.528A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.874A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.593A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 543 through 546 Processing helix chain 'A' and resid 616 through 627 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.718A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.272A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.860A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.530A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.783A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.524A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.598A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 30 removed outlier: 8.716A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.829A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.883A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.856A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.195A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.822A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.104A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.858A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.449A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 712 through 713 removed outlier: 4.042A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 717 through 722 removed outlier: 3.533A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 717 through 722 removed outlier: 3.533A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.519A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.889A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.508A pdb=" N PHE C 43 " --> pdb=" O PHE A 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.928A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.966A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.077A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.631A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.313A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.672A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.746A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 664 through 667 removed outlier: 3.503A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.507A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AD4, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.285A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.595A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 787 through 788 removed outlier: 3.689A pdb=" N ILE C 788 " --> pdb=" O ALA A 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, 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=AD8, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.754A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.788A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.648A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.778A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.162A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.972A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.891A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.299A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.170A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.684A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.939A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 717 through 722 Processing sheet with id=AF2, first strand: chain 'A' and resid 717 through 722 removed outlier: 7.326A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.497A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AF5, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.146A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.146A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 108 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AG1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.628A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.628A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.505A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 11 through 12 removed outlier: 7.168A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.329A pdb=" N TYR D 111 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLU D 100 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE D 109 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.897A pdb=" N GLU E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.796A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2628 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: 6.92 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6269 1.33 - 1.46: 7993 1.46 - 1.58: 15681 1.58 - 1.71: 0 1.71 - 1.83: 161 Bond restraints: 30104 Sorted by residual: bond pdb=" CA SER B1097 " pdb=" CB SER B1097 " ideal model delta sigma weight residual 1.533 1.449 0.084 1.69e-02 3.50e+03 2.49e+01 bond pdb=" CA SER B 305 " pdb=" CB SER B 305 " ideal model delta sigma weight residual 1.532 1.464 0.068 1.68e-02 3.54e+03 1.66e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.43e+01 bond pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta sigma weight residual 1.456 1.486 -0.031 8.70e-03 1.32e+04 1.25e+01 bond pdb=" N ILE H 103 " pdb=" CA ILE H 103 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 ... (remaining 30099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 39436 2.02 - 4.03: 1331 4.03 - 6.05: 156 6.05 - 8.06: 35 8.06 - 10.08: 3 Bond angle restraints: 40961 Sorted by residual: angle pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" C THR B 299 " ideal model delta sigma weight residual 112.54 103.42 9.12 1.22e+00 6.72e-01 5.59e+01 angle pdb=" N THR B 302 " pdb=" CA THR B 302 " pdb=" C THR B 302 " ideal model delta sigma weight residual 113.41 105.93 7.48 1.22e+00 6.72e-01 3.76e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 117.17 -6.47 1.22e+00 6.72e-01 2.81e+01 angle pdb=" N LYS B 300 " pdb=" CA LYS B 300 " pdb=" C LYS B 300 " ideal model delta sigma weight residual 113.28 107.37 5.91 1.22e+00 6.72e-01 2.35e+01 angle pdb=" N LEU B 303 " pdb=" CA LEU B 303 " pdb=" C LEU B 303 " ideal model delta sigma weight residual 113.15 107.47 5.68 1.19e+00 7.06e-01 2.28e+01 ... (remaining 40956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 16681 23.12 - 46.24: 1661 46.24 - 69.36: 207 69.36 - 92.48: 105 92.48 - 115.60: 75 Dihedral angle restraints: 18729 sinusoidal: 8139 harmonic: 10590 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -13.83 -72.17 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 31.70 61.30 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -146.26 60.26 1 1.00e+01 1.00e-02 4.84e+01 ... (remaining 18726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 4773 0.198 - 0.396: 21 0.396 - 0.594: 2 0.594 - 0.792: 1 0.792 - 0.990: 1 Chirality restraints: 4798 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.51e+00 ... (remaining 4795 not shown) Planarity restraints: 5255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.091 2.00e-02 2.50e+03 7.45e-02 6.94e+01 pdb=" C7 NAG I 1 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.119 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 237 " -0.564 9.50e-02 1.11e+02 2.53e-01 3.90e+01 pdb=" NE ARG A 237 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 237 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 237 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 237 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.061 2.00e-02 2.50e+03 5.03e-02 3.16e+01 pdb=" C7 NAG A1301 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.046 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.081 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.009 2.00e-02 2.50e+03 ... (remaining 5252 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2663 2.74 - 3.28: 28437 3.28 - 3.82: 46213 3.82 - 4.36: 52821 4.36 - 4.90: 93487 Nonbonded interactions: 223621 Sorted by model distance: nonbonded pdb=" NH1 ARG A 454 " pdb=" O ASP A 467 " model vdw 2.203 3.120 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.207 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.209 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR C 912 " pdb=" OD1 ASN C 914 " model vdw 2.230 3.040 ... (remaining 223616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 1312) selection = (chain 'B' and resid 23 through 1312) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.800 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 30210 Z= 0.275 Angle : 0.830 18.233 41239 Z= 0.466 Chirality : 0.055 0.990 4798 Planarity : 0.008 0.253 5201 Dihedral : 19.323 115.597 11828 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.67 % Favored : 91.91 % Rotamer: Outliers : 0.82 % Allowed : 25.17 % Favored : 74.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.14), residues: 3611 helix: 0.93 (0.21), residues: 682 sheet: -0.79 (0.18), residues: 836 loop : -2.15 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 16 TYR 0.027 0.001 TYR A 495 PHE 0.043 0.001 PHE C 135 TRP 0.040 0.002 TRP C 633 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00469 (30104) covalent geometry : angle 0.80915 (40961) SS BOND : bond 0.00307 ( 37) SS BOND : angle 1.28109 ( 74) hydrogen bonds : bond 0.22066 ( 954) hydrogen bonds : angle 8.19255 ( 2628) Misc. bond : bond 0.00014 ( 1) link_BETA1-4 : bond 0.00575 ( 14) link_BETA1-4 : angle 2.10178 ( 42) link_NAG-ASN : bond 0.00661 ( 54) link_NAG-ASN : angle 2.83706 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 291 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 934 ILE cc_start: 0.8652 (tt) cc_final: 0.8367 (tp) REVERT: A 196 ASN cc_start: 0.8783 (t0) cc_final: 0.8574 (t0) REVERT: A 487 ASN cc_start: 0.3613 (OUTLIER) cc_final: 0.2393 (t0) REVERT: A 984 LEU cc_start: 0.7962 (tp) cc_final: 0.7711 (tp) REVERT: D 16 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.7954 (mtt180) REVERT: E 4 MET cc_start: 0.6494 (mmt) cc_final: 0.6169 (tpt) outliers start: 26 outliers final: 10 residues processed: 309 average time/residue: 0.1917 time to fit residues: 95.9207 Evaluate side-chains 261 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 86 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 628 GLN C 774 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN L 32 ASN L 92 ASN D 77 ASN E 32 ASN E 79 GLN E 92 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.173970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127590 restraints weight = 48971.626| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 4.09 r_work: 0.3366 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30210 Z= 0.229 Angle : 0.764 17.484 41239 Z= 0.381 Chirality : 0.051 0.772 4798 Planarity : 0.006 0.086 5201 Dihedral : 10.539 108.882 5353 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.64 % Favored : 91.19 % Rotamer: Outliers : 4.34 % Allowed : 23.07 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3611 helix: 0.76 (0.20), residues: 697 sheet: -0.67 (0.18), residues: 880 loop : -2.24 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1107 TYR 0.027 0.002 TYR A1067 PHE 0.022 0.002 PHE C 86 TRP 0.018 0.002 TRP C 633 HIS 0.006 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00551 (30104) covalent geometry : angle 0.73835 (40961) SS BOND : bond 0.00413 ( 37) SS BOND : angle 1.53183 ( 74) hydrogen bonds : bond 0.06253 ( 954) hydrogen bonds : angle 5.85993 ( 2628) Misc. bond : bond 0.00053 ( 1) link_BETA1-4 : bond 0.00663 ( 14) link_BETA1-4 : angle 2.95032 ( 42) link_NAG-ASN : bond 0.00477 ( 54) link_NAG-ASN : angle 2.73608 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 290 time to evaluate : 1.087 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: B 329 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: B 1141 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6707 (mp) REVERT: C 129 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.6885 (tttp) REVERT: C 135 PHE cc_start: 0.6953 (t80) cc_final: 0.6420 (t80) REVERT: C 200 TYR cc_start: 0.7394 (m-80) cc_final: 0.7068 (m-80) REVERT: C 940 SER cc_start: 0.8644 (m) cc_final: 0.8236 (p) REVERT: A 242 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7290 (mm) REVERT: A 265 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: A 487 ASN cc_start: 0.2218 (OUTLIER) cc_final: 0.1577 (t0) REVERT: A 492 LEU cc_start: 0.1032 (OUTLIER) cc_final: 0.0711 (tp) REVERT: A 619 GLU cc_start: 0.8068 (tt0) cc_final: 0.7774 (tt0) REVERT: H 106 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8442 (p90) REVERT: L 11 LEU cc_start: 0.6461 (tp) cc_final: 0.6051 (mp) REVERT: D 16 ARG cc_start: 0.8959 (mmm-85) cc_final: 0.8755 (mmm-85) REVERT: D 73 ASP cc_start: 0.8693 (t0) cc_final: 0.8450 (t0) REVERT: D 76 LYS cc_start: 0.9164 (mtpt) cc_final: 0.8707 (mtpp) REVERT: D 106 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.6931 (p90) REVERT: E 4 MET cc_start: 0.5997 (mmt) cc_final: 0.5310 (mmm) REVERT: E 38 GLN cc_start: 0.5335 (tp40) cc_final: 0.4543 (tt0) REVERT: E 54 ARG cc_start: 0.7292 (ttm110) cc_final: 0.7035 (ttm170) outliers start: 137 outliers final: 71 residues processed: 397 average time/residue: 0.1782 time to fit residues: 117.6367 Evaluate side-chains 328 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 248 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 289 optimal weight: 0.0370 chunk 191 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 352 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 282 optimal weight: 0.7980 chunk 235 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C 978 ASN A 87 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 HIS D 35 HIS E 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.175184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129231 restraints weight = 48988.370| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.73 r_work: 0.3407 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30210 Z= 0.117 Angle : 0.627 16.893 41239 Z= 0.311 Chirality : 0.046 0.689 4798 Planarity : 0.005 0.077 5201 Dihedral : 7.836 104.942 5344 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.14 % Favored : 92.72 % Rotamer: Outliers : 3.26 % Allowed : 25.13 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3611 helix: 1.15 (0.21), residues: 703 sheet: -0.50 (0.18), residues: 894 loop : -2.16 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.020 0.001 TYR B1067 PHE 0.021 0.001 PHE A 135 TRP 0.016 0.001 TRP C 436 HIS 0.009 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00256 (30104) covalent geometry : angle 0.60196 (40961) SS BOND : bond 0.00324 ( 37) SS BOND : angle 1.13302 ( 74) hydrogen bonds : bond 0.04829 ( 954) hydrogen bonds : angle 5.33608 ( 2628) Misc. bond : bond 0.00048 ( 1) link_BETA1-4 : bond 0.00572 ( 14) link_BETA1-4 : angle 2.58316 ( 42) link_NAG-ASN : bond 0.00408 ( 54) link_NAG-ASN : angle 2.45887 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 282 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8189 (p0) REVERT: B 278 LYS cc_start: 0.9301 (tptt) cc_final: 0.8855 (tttt) REVERT: B 329 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.5998 (m-10) REVERT: B 633 TRP cc_start: 0.7536 (p90) cc_final: 0.6712 (p90) REVERT: B 1141 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6661 (mp) REVERT: C 135 PHE cc_start: 0.6740 (t80) cc_final: 0.6284 (t80) REVERT: C 200 TYR cc_start: 0.7252 (m-80) cc_final: 0.6976 (m-80) REVERT: C 238 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8183 (t80) REVERT: C 778 THR cc_start: 0.9017 (t) cc_final: 0.8714 (m) REVERT: C 940 SER cc_start: 0.8617 (m) cc_final: 0.8145 (p) REVERT: A 135 PHE cc_start: 0.7255 (t80) cc_final: 0.6958 (t80) REVERT: A 242 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 487 ASN cc_start: 0.2890 (OUTLIER) cc_final: 0.2053 (t0) REVERT: A 619 GLU cc_start: 0.8130 (tt0) cc_final: 0.7914 (tt0) REVERT: A 697 MET cc_start: 0.8631 (mtp) cc_final: 0.8428 (mtm) REVERT: A 775 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: H 106 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8293 (p90) REVERT: L 11 LEU cc_start: 0.6620 (tp) cc_final: 0.6236 (mp) REVERT: L 54 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7956 (mtm110) REVERT: D 101 PRO cc_start: 0.8854 (Cg_exo) cc_final: 0.8618 (Cg_endo) REVERT: E 4 MET cc_start: 0.6093 (mmt) cc_final: 0.5423 (mmm) REVERT: E 71 PHE cc_start: 0.7887 (m-80) cc_final: 0.7494 (m-80) outliers start: 103 outliers final: 51 residues processed: 366 average time/residue: 0.1806 time to fit residues: 110.1713 Evaluate side-chains 314 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 290 optimal weight: 0.0010 chunk 33 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 313 optimal weight: 0.5980 chunk 349 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 121 ASN B 506 GLN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 774 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 774 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.172064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124225 restraints weight = 48455.936| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.71 r_work: 0.3377 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30210 Z= 0.142 Angle : 0.628 16.756 41239 Z= 0.314 Chirality : 0.046 0.682 4798 Planarity : 0.005 0.080 5201 Dihedral : 6.636 98.439 5341 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.00 % Favored : 91.86 % Rotamer: Outliers : 4.47 % Allowed : 24.28 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3611 helix: 1.26 (0.21), residues: 700 sheet: -0.45 (0.18), residues: 870 loop : -2.10 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.021 0.001 TYR A 904 PHE 0.015 0.001 PHE B 329 TRP 0.027 0.002 TRP L 35 HIS 0.018 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00334 (30104) covalent geometry : angle 0.60506 (40961) SS BOND : bond 0.00307 ( 37) SS BOND : angle 1.23049 ( 74) hydrogen bonds : bond 0.05003 ( 954) hydrogen bonds : angle 5.12441 ( 2628) Misc. bond : bond 0.00042 ( 1) link_BETA1-4 : bond 0.00444 ( 14) link_BETA1-4 : angle 2.25694 ( 42) link_NAG-ASN : bond 0.00362 ( 54) link_NAG-ASN : angle 2.42981 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 263 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8262 (t) REVERT: B 179 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.4575 (pp) REVERT: B 246 ARG cc_start: 0.5097 (OUTLIER) cc_final: 0.3678 (mmm160) REVERT: B 264 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8201 (p0) REVERT: B 298 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: B 329 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6083 (m-10) REVERT: B 720 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8826 (mt) REVERT: B 1141 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6644 (mp) REVERT: C 135 PHE cc_start: 0.6867 (t80) cc_final: 0.6298 (t80) REVERT: C 200 TYR cc_start: 0.7241 (m-80) cc_final: 0.7023 (m-80) REVERT: C 238 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8102 (t80) REVERT: C 778 THR cc_start: 0.8994 (t) cc_final: 0.8744 (m) REVERT: C 918 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: C 940 SER cc_start: 0.8499 (m) cc_final: 0.7999 (p) REVERT: A 135 PHE cc_start: 0.6960 (t80) cc_final: 0.6647 (t80) REVERT: A 238 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 242 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7365 (mm) REVERT: A 265 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: A 487 ASN cc_start: 0.2755 (OUTLIER) cc_final: 0.1980 (t0) REVERT: A 775 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: H 106 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8167 (p90) REVERT: L 11 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6240 (mp) REVERT: L 54 ARG cc_start: 0.8413 (mtm110) cc_final: 0.7965 (mtm110) REVERT: D 16 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.7896 (mtm110) REVERT: D 83 MET cc_start: 0.8240 (mtm) cc_final: 0.7926 (mtm) REVERT: E 4 MET cc_start: 0.5979 (mmt) cc_final: 0.5347 (mmm) outliers start: 141 outliers final: 78 residues processed: 377 average time/residue: 0.1781 time to fit residues: 112.3502 Evaluate side-chains 339 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 244 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 50 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 304 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 357 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 360 optimal weight: 9.9990 chunk 261 optimal weight: 0.0970 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 978 ASN A 81 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 38 GLN E 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.174828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128761 restraints weight = 48818.544| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.22 r_work: 0.3387 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30210 Z= 0.112 Angle : 0.592 16.120 41239 Z= 0.295 Chirality : 0.045 0.664 4798 Planarity : 0.004 0.075 5201 Dihedral : 6.131 94.965 5341 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.14 % Favored : 92.72 % Rotamer: Outliers : 3.99 % Allowed : 24.98 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3611 helix: 1.40 (0.21), residues: 704 sheet: -0.41 (0.18), residues: 852 loop : -2.02 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 54 TYR 0.018 0.001 TYR B1067 PHE 0.026 0.001 PHE B 65 TRP 0.025 0.001 TRP L 35 HIS 0.008 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00251 (30104) covalent geometry : angle 0.57093 (40961) SS BOND : bond 0.00386 ( 37) SS BOND : angle 1.03322 ( 74) hydrogen bonds : bond 0.04296 ( 954) hydrogen bonds : angle 4.89361 ( 2628) Misc. bond : bond 0.00041 ( 1) link_BETA1-4 : bond 0.00513 ( 14) link_BETA1-4 : angle 1.93832 ( 42) link_NAG-ASN : bond 0.00370 ( 54) link_NAG-ASN : angle 2.30728 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 270 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8229 (t) REVERT: B 179 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4449 (pp) REVERT: B 264 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8269 (p0) REVERT: B 298 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7059 (mt-10) REVERT: B 327 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7756 (t) REVERT: B 329 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.5998 (m-10) REVERT: B 754 LEU cc_start: 0.9030 (tp) cc_final: 0.8755 (tt) REVERT: B 1141 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6538 (mp) REVERT: C 135 PHE cc_start: 0.6850 (t80) cc_final: 0.6210 (t80) REVERT: C 200 TYR cc_start: 0.7188 (m-80) cc_final: 0.6962 (m-80) REVERT: C 778 THR cc_start: 0.8872 (t) cc_final: 0.8569 (m) REVERT: C 779 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: A 66 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7233 (t-90) REVERT: A 135 PHE cc_start: 0.6988 (t80) cc_final: 0.6697 (t80) REVERT: A 238 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7669 (t80) REVERT: A 242 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7793 (mm) REVERT: A 269 TYR cc_start: 0.8742 (m-80) cc_final: 0.8351 (m-80) REVERT: A 487 ASN cc_start: 0.2492 (OUTLIER) cc_final: 0.1843 (t0) REVERT: A 775 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: A 780 GLU cc_start: 0.8446 (tt0) cc_final: 0.8199 (tt0) REVERT: A 984 LEU cc_start: 0.8051 (mm) cc_final: 0.7777 (mp) REVERT: H 106 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8074 (p90) REVERT: L 11 LEU cc_start: 0.6555 (tp) cc_final: 0.6232 (mp) REVERT: L 54 ARG cc_start: 0.8366 (mtm110) cc_final: 0.7975 (mtm110) REVERT: E 4 MET cc_start: 0.5859 (mmt) cc_final: 0.5256 (mmm) REVERT: E 38 GLN cc_start: 0.5522 (OUTLIER) cc_final: 0.4421 (tt0) REVERT: E 71 PHE cc_start: 0.7924 (m-80) cc_final: 0.7456 (m-80) REVERT: E 90 GLN cc_start: 0.8463 (pp30) cc_final: 0.8251 (pp30) outliers start: 126 outliers final: 69 residues processed: 376 average time/residue: 0.1722 time to fit residues: 108.3230 Evaluate side-chains 321 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 238 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 38 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 220 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 chunk 327 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 HIS B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN E 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.172742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126171 restraints weight = 48618.108| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 4.21 r_work: 0.3352 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 30210 Z= 0.139 Angle : 0.614 16.168 41239 Z= 0.306 Chirality : 0.046 0.662 4798 Planarity : 0.005 0.089 5201 Dihedral : 6.031 93.737 5341 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.53 % Favored : 92.33 % Rotamer: Outliers : 4.66 % Allowed : 23.90 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.14), residues: 3611 helix: 1.41 (0.21), residues: 705 sheet: -0.54 (0.18), residues: 886 loop : -1.99 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.001 PHE A 643 TRP 0.024 0.001 TRP L 35 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00332 (30104) covalent geometry : angle 0.59135 (40961) SS BOND : bond 0.00268 ( 37) SS BOND : angle 1.38834 ( 74) hydrogen bonds : bond 0.04779 ( 954) hydrogen bonds : angle 4.92269 ( 2628) Misc. bond : bond 0.00035 ( 1) link_BETA1-4 : bond 0.00451 ( 14) link_BETA1-4 : angle 1.90601 ( 42) link_NAG-ASN : bond 0.00326 ( 54) link_NAG-ASN : angle 2.36761 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 248 time to evaluate : 1.116 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: B 33 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8415 (t) REVERT: B 135 PHE cc_start: 0.7353 (p90) cc_final: 0.6342 (t80) REVERT: B 179 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4529 (pp) REVERT: B 246 ARG cc_start: 0.5120 (OUTLIER) cc_final: 0.3641 (mmm160) REVERT: B 264 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8283 (p0) REVERT: B 298 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: B 327 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.7897 (t) REVERT: B 329 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.5961 (m-10) REVERT: B 754 LEU cc_start: 0.9042 (tp) cc_final: 0.8793 (tt) REVERT: B 1141 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6364 (mp) REVERT: C 135 PHE cc_start: 0.6970 (t80) cc_final: 0.6231 (t80) REVERT: C 200 TYR cc_start: 0.7353 (m-80) cc_final: 0.7142 (m-80) REVERT: C 238 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8159 (t80) REVERT: C 489 TYR cc_start: 0.2009 (OUTLIER) cc_final: 0.0978 (m-80) REVERT: C 778 THR cc_start: 0.8998 (t) cc_final: 0.8750 (m) REVERT: C 779 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: C 918 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: A 40 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8210 (p0) REVERT: A 66 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7376 (t-90) REVERT: A 135 PHE cc_start: 0.6940 (t80) cc_final: 0.6710 (t80) REVERT: A 238 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7800 (t80) REVERT: A 242 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7453 (mm) REVERT: A 265 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: A 487 ASN cc_start: 0.2684 (OUTLIER) cc_final: 0.2026 (t0) REVERT: A 775 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: A 780 GLU cc_start: 0.8481 (tt0) cc_final: 0.8275 (tt0) REVERT: A 984 LEU cc_start: 0.8068 (mm) cc_final: 0.7808 (mp) REVERT: H 106 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8062 (p90) REVERT: L 54 ARG cc_start: 0.8370 (mtm110) cc_final: 0.7987 (mtm110) REVERT: D 16 ARG cc_start: 0.8870 (mmm-85) cc_final: 0.7900 (mtm110) REVERT: E 38 GLN cc_start: 0.5321 (OUTLIER) cc_final: 0.4551 (tt0) outliers start: 147 outliers final: 95 residues processed: 366 average time/residue: 0.1804 time to fit residues: 109.5815 Evaluate side-chains 354 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 238 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 158 optimal weight: 1.9990 chunk 253 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 105 optimal weight: 0.0010 chunk 32 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN A 87 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN E 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.171313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124459 restraints weight = 48711.050| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 4.18 r_work: 0.3343 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 30210 Z= 0.144 Angle : 0.624 15.933 41239 Z= 0.311 Chirality : 0.046 0.655 4798 Planarity : 0.005 0.083 5201 Dihedral : 5.942 88.283 5341 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.81 % Favored : 92.05 % Rotamer: Outliers : 4.88 % Allowed : 23.87 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3611 helix: 1.45 (0.21), residues: 701 sheet: -0.51 (0.18), residues: 886 loop : -1.98 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE B 133 TRP 0.019 0.001 TRP L 35 HIS 0.009 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00347 (30104) covalent geometry : angle 0.60123 (40961) SS BOND : bond 0.00284 ( 37) SS BOND : angle 1.71450 ( 74) hydrogen bonds : bond 0.04884 ( 954) hydrogen bonds : angle 4.93976 ( 2628) Misc. bond : bond 0.00037 ( 1) link_BETA1-4 : bond 0.00454 ( 14) link_BETA1-4 : angle 1.86206 ( 42) link_NAG-ASN : bond 0.00325 ( 54) link_NAG-ASN : angle 2.35570 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 253 time to evaluate : 1.078 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: B 135 PHE cc_start: 0.7405 (p90) cc_final: 0.6460 (t80) REVERT: B 179 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4520 (pp) REVERT: B 246 ARG cc_start: 0.5233 (OUTLIER) cc_final: 0.3560 (mmm160) REVERT: B 298 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: B 327 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.7796 (t) REVERT: B 329 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6036 (m-10) REVERT: B 754 LEU cc_start: 0.9072 (tp) cc_final: 0.8847 (tt) REVERT: C 135 PHE cc_start: 0.7021 (t80) cc_final: 0.6175 (t80) REVERT: C 238 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8185 (t80) REVERT: C 489 TYR cc_start: 0.2052 (OUTLIER) cc_final: 0.1007 (m-80) REVERT: C 529 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8563 (ttmm) REVERT: C 778 THR cc_start: 0.8951 (t) cc_final: 0.8725 (m) REVERT: C 779 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: C 918 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: A 66 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7439 (t-90) REVERT: A 135 PHE cc_start: 0.6908 (t80) cc_final: 0.6646 (t80) REVERT: A 238 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7888 (t80) REVERT: A 242 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7440 (mm) REVERT: A 265 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: A 487 ASN cc_start: 0.2716 (OUTLIER) cc_final: 0.2067 (t0) REVERT: A 775 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: A 984 LEU cc_start: 0.8092 (mm) cc_final: 0.7839 (mp) REVERT: H 106 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7744 (p90) REVERT: L 54 ARG cc_start: 0.8385 (mtm110) cc_final: 0.7979 (mtm110) REVERT: D 16 ARG cc_start: 0.8910 (mmm-85) cc_final: 0.7957 (mtm110) REVERT: D 83 MET cc_start: 0.8336 (mtm) cc_final: 0.7941 (mtm) REVERT: E 38 GLN cc_start: 0.5030 (OUTLIER) cc_final: 0.4516 (tt0) REVERT: E 71 PHE cc_start: 0.7822 (m-80) cc_final: 0.7482 (m-80) outliers start: 154 outliers final: 102 residues processed: 381 average time/residue: 0.1757 time to fit residues: 111.5184 Evaluate side-chains 358 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 239 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 208 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 129 optimal weight: 0.0170 chunk 201 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 325 optimal weight: 6.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 HIS B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN E 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.173249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126590 restraints weight = 48695.693| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.17 r_work: 0.3369 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30210 Z= 0.113 Angle : 0.609 15.587 41239 Z= 0.302 Chirality : 0.046 0.648 4798 Planarity : 0.004 0.076 5201 Dihedral : 5.746 86.572 5341 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.62 % Favored : 92.25 % Rotamer: Outliers : 3.99 % Allowed : 24.75 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3611 helix: 1.56 (0.21), residues: 701 sheet: -0.47 (0.18), residues: 900 loop : -1.91 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 102 TYR 0.019 0.001 TYR B 495 PHE 0.012 0.001 PHE A 643 TRP 0.020 0.001 TRP C 436 HIS 0.011 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00259 (30104) covalent geometry : angle 0.58729 (40961) SS BOND : bond 0.00269 ( 37) SS BOND : angle 1.60047 ( 74) hydrogen bonds : bond 0.04329 ( 954) hydrogen bonds : angle 4.82386 ( 2628) Misc. bond : bond 0.00035 ( 1) link_BETA1-4 : bond 0.00528 ( 14) link_BETA1-4 : angle 1.81785 ( 42) link_NAG-ASN : bond 0.00368 ( 54) link_NAG-ASN : angle 2.28637 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 256 time to evaluate : 1.103 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: B 41 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7304 (mttp) REVERT: B 135 PHE cc_start: 0.7388 (p90) cc_final: 0.6448 (t80) REVERT: B 179 LEU cc_start: 0.4813 (OUTLIER) cc_final: 0.4470 (pp) REVERT: B 246 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.3645 (mmm160) REVERT: B 327 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.7950 (t) REVERT: B 329 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6049 (m-10) REVERT: B 754 LEU cc_start: 0.9123 (tp) cc_final: 0.8891 (tt) REVERT: C 135 PHE cc_start: 0.6896 (t80) cc_final: 0.6133 (t80) REVERT: C 238 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8284 (t80) REVERT: C 489 TYR cc_start: 0.2110 (OUTLIER) cc_final: 0.1045 (m-80) REVERT: C 529 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8571 (ttmm) REVERT: C 778 THR cc_start: 0.8880 (t) cc_final: 0.8571 (m) REVERT: C 779 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: C 918 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: A 66 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7487 (t-90) REVERT: A 135 PHE cc_start: 0.6732 (t80) cc_final: 0.6516 (t80) REVERT: A 238 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7776 (t80) REVERT: A 242 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7428 (mm) REVERT: A 265 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: A 269 TYR cc_start: 0.8753 (m-80) cc_final: 0.8352 (m-80) REVERT: A 480 CYS cc_start: 0.1952 (OUTLIER) cc_final: 0.1428 (t) REVERT: A 487 ASN cc_start: 0.2878 (OUTLIER) cc_final: 0.2204 (t0) REVERT: A 775 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: A 984 LEU cc_start: 0.8070 (mm) cc_final: 0.7831 (mp) REVERT: A 1029 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8188 (ttp) REVERT: H 106 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8063 (p90) REVERT: L 54 ARG cc_start: 0.8382 (mtm110) cc_final: 0.8063 (mtm110) REVERT: D 16 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.7996 (mtm110) REVERT: E 4 MET cc_start: 0.5801 (mmt) cc_final: 0.5218 (mmm) REVERT: E 38 GLN cc_start: 0.5385 (OUTLIER) cc_final: 0.4588 (tt0) REVERT: E 71 PHE cc_start: 0.7815 (m-80) cc_final: 0.7496 (m-80) REVERT: E 90 GLN cc_start: 0.8529 (pp30) cc_final: 0.8266 (pp30) outliers start: 126 outliers final: 90 residues processed: 353 average time/residue: 0.1764 time to fit residues: 103.2968 Evaluate side-chains 350 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 241 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 394 ASN B 625 HIS B 804 GLN B 901 GLN B 935 GLN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.170472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123738 restraints weight = 48806.639| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.61 r_work: 0.3340 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 30210 Z= 0.163 Angle : 0.641 15.664 41239 Z= 0.321 Chirality : 0.046 0.650 4798 Planarity : 0.005 0.076 5201 Dihedral : 5.826 84.850 5341 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.56 % Favored : 91.30 % Rotamer: Outliers : 4.06 % Allowed : 24.94 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3611 helix: 1.50 (0.21), residues: 695 sheet: -0.47 (0.18), residues: 908 loop : -1.97 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.021 0.001 TYR B 265 PHE 0.015 0.001 PHE C 86 TRP 0.022 0.002 TRP B 633 HIS 0.011 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00400 (30104) covalent geometry : angle 0.61947 (40961) SS BOND : bond 0.00303 ( 37) SS BOND : angle 1.70226 ( 74) hydrogen bonds : bond 0.05236 ( 954) hydrogen bonds : angle 4.94355 ( 2628) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00433 ( 14) link_BETA1-4 : angle 1.83468 ( 42) link_NAG-ASN : bond 0.00313 ( 54) link_NAG-ASN : angle 2.33459 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 244 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 PHE cc_start: 0.7424 (p90) cc_final: 0.6443 (t80) REVERT: B 179 LEU cc_start: 0.4683 (OUTLIER) cc_final: 0.4327 (pp) REVERT: B 246 ARG cc_start: 0.4915 (OUTLIER) cc_final: 0.3157 (mmm160) REVERT: B 327 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.7914 (t) REVERT: B 329 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6111 (m-10) REVERT: B 616 ASN cc_start: 0.7495 (t0) cc_final: 0.6731 (p0) REVERT: B 633 TRP cc_start: 0.8059 (p90) cc_final: 0.7668 (p90) REVERT: B 754 LEU cc_start: 0.9108 (tp) cc_final: 0.8901 (tt) REVERT: C 135 PHE cc_start: 0.7103 (t80) cc_final: 0.6310 (t80) REVERT: C 238 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8026 (t80) REVERT: C 489 TYR cc_start: 0.2256 (OUTLIER) cc_final: 0.1139 (m-80) REVERT: C 529 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8580 (ttmm) REVERT: C 661 GLU cc_start: 0.8304 (mp0) cc_final: 0.8102 (pm20) REVERT: C 778 THR cc_start: 0.8994 (t) cc_final: 0.8773 (m) REVERT: C 779 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: C 918 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: A 66 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: A 135 PHE cc_start: 0.6741 (t80) cc_final: 0.6520 (t80) REVERT: A 238 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7982 (t80) REVERT: A 242 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7405 (mm) REVERT: A 265 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: A 487 ASN cc_start: 0.2876 (OUTLIER) cc_final: 0.2199 (t0) REVERT: A 646 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7347 (mpt180) REVERT: A 775 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: A 984 LEU cc_start: 0.8143 (mm) cc_final: 0.7937 (mp) REVERT: H 106 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.7784 (p90) REVERT: L 54 ARG cc_start: 0.8368 (mtm110) cc_final: 0.8051 (mtm110) REVERT: E 4 MET cc_start: 0.5935 (mmt) cc_final: 0.5638 (mmm) REVERT: E 38 GLN cc_start: 0.4775 (OUTLIER) cc_final: 0.4509 (tt0) REVERT: E 71 PHE cc_start: 0.7778 (m-80) cc_final: 0.7453 (m-80) REVERT: E 90 GLN cc_start: 0.8570 (pp30) cc_final: 0.8282 (pp30) outliers start: 128 outliers final: 96 residues processed: 351 average time/residue: 0.1757 time to fit residues: 102.6188 Evaluate side-chains 353 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 240 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 77 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 307 optimal weight: 0.0000 chunk 173 optimal weight: 0.7980 chunk 352 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 625 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.169350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122741 restraints weight = 48366.045| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.82 r_work: 0.3298 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30210 Z= 0.179 Angle : 0.656 15.668 41239 Z= 0.327 Chirality : 0.047 0.648 4798 Planarity : 0.005 0.075 5201 Dihedral : 5.912 84.833 5341 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.34 % Favored : 91.53 % Rotamer: Outliers : 3.93 % Allowed : 25.01 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3611 helix: 1.48 (0.21), residues: 695 sheet: -0.47 (0.17), residues: 912 loop : -2.02 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 16 TYR 0.020 0.001 TYR A1067 PHE 0.032 0.001 PHE A 86 TRP 0.020 0.002 TRP L 35 HIS 0.011 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00437 (30104) covalent geometry : angle 0.63403 (40961) SS BOND : bond 0.00389 ( 37) SS BOND : angle 1.80236 ( 74) hydrogen bonds : bond 0.05374 ( 954) hydrogen bonds : angle 4.99702 ( 2628) Misc. bond : bond 0.00029 ( 1) link_BETA1-4 : bond 0.00455 ( 14) link_BETA1-4 : angle 1.82656 ( 42) link_NAG-ASN : bond 0.00314 ( 54) link_NAG-ASN : angle 2.36917 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7222 Ramachandran restraints generated. 3611 Oldfield, 0 Emsley, 3611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 245 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7378 (mttp) REVERT: B 135 PHE cc_start: 0.7443 (p90) cc_final: 0.6529 (t80) REVERT: B 179 LEU cc_start: 0.4623 (OUTLIER) cc_final: 0.4272 (pp) REVERT: B 246 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.3127 (mmm160) REVERT: B 327 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.7977 (t) REVERT: B 329 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6178 (m-10) REVERT: B 616 ASN cc_start: 0.7442 (t0) cc_final: 0.6709 (p0) REVERT: B 625 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6994 (m170) REVERT: B 633 TRP cc_start: 0.8131 (p90) cc_final: 0.7723 (p90) REVERT: B 754 LEU cc_start: 0.9114 (tp) cc_final: 0.8907 (tt) REVERT: C 238 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.7896 (t80) REVERT: C 489 TYR cc_start: 0.2187 (OUTLIER) cc_final: 0.1151 (m-80) REVERT: C 529 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8606 (ttmm) REVERT: C 661 GLU cc_start: 0.8382 (mp0) cc_final: 0.8178 (pm20) REVERT: C 778 THR cc_start: 0.9034 (t) cc_final: 0.8819 (m) REVERT: C 779 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: C 918 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: A 40 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8238 (p0) REVERT: A 66 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7633 (t-90) REVERT: A 135 PHE cc_start: 0.6732 (t80) cc_final: 0.6516 (t80) REVERT: A 242 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7452 (mm) REVERT: A 265 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: A 487 ASN cc_start: 0.2774 (OUTLIER) cc_final: 0.2234 (t0) REVERT: A 775 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: H 106 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.7710 (p90) REVERT: L 54 ARG cc_start: 0.8398 (mtm110) cc_final: 0.8048 (mtm110) REVERT: E 4 MET cc_start: 0.5896 (mmt) cc_final: 0.5568 (mmm) REVERT: E 38 GLN cc_start: 0.5561 (OUTLIER) cc_final: 0.4805 (tt0) REVERT: E 71 PHE cc_start: 0.7671 (m-80) cc_final: 0.7273 (m-80) REVERT: E 90 GLN cc_start: 0.8627 (pp30) cc_final: 0.8323 (pp30) outliers start: 124 outliers final: 98 residues processed: 348 average time/residue: 0.1713 time to fit residues: 100.0293 Evaluate side-chains 359 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 243 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 149 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 0.4980 chunk 120 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 229 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 625 HIS B 901 GLN C 388 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.122281 restraints weight = 48750.705| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 4.07 r_work: 0.3318 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30210 Z= 0.122 Angle : 0.619 15.304 41239 Z= 0.308 Chirality : 0.046 0.643 4798 Planarity : 0.004 0.073 5201 Dihedral : 5.751 84.669 5341 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.03 % Favored : 91.86 % Rotamer: Outliers : 3.77 % Allowed : 25.29 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3611 helix: 1.58 (0.21), residues: 695 sheet: -0.40 (0.18), residues: 903 loop : -1.96 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 16 TYR 0.018 0.001 TYR B 265 PHE 0.013 0.001 PHE B 643 TRP 0.019 0.001 TRP C 436 HIS 0.019 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00281 (30104) covalent geometry : angle 0.59828 (40961) SS BOND : bond 0.00276 ( 37) SS BOND : angle 1.57332 ( 74) hydrogen bonds : bond 0.04695 ( 954) hydrogen bonds : angle 4.88280 ( 2628) Misc. bond : bond 0.00027 ( 1) link_BETA1-4 : bond 0.00503 ( 14) link_BETA1-4 : angle 1.78654 ( 42) link_NAG-ASN : bond 0.00331 ( 54) link_NAG-ASN : angle 2.28619 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7440.00 seconds wall clock time: 128 minutes 8.68 seconds (7688.68 seconds total)