Starting phenix.real_space_refine on Wed Jun 25 09:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y4a_38914/06_2025/8y4a_38914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y4a_38914/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y4a_38914/06_2025/8y4a_38914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y4a_38914/06_2025/8y4a_38914.map" model { file = "/net/cci-nas-00/data/ceres_data/8y4a_38914/06_2025/8y4a_38914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y4a_38914/06_2025/8y4a_38914.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 1.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.84, per 1000 atoms: 0.61 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: 7.27 Conformation dependent library (CDL) restraints added in 3.5 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: 4.72 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: 13.90 Time building geometry restraints manager: 8.67 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 1144 or resid 1301 through 1312)) selection = (chain 'B' and (resid 23 through 1144 or resid 1301 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 69.080 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.420 ------------------------------------------------------------------------------- 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 : 9.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (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 TRP 0.040 0.002 TRP C 633 HIS 0.005 0.001 HIS D 35 PHE 0.043 0.001 PHE C 135 TYR 0.027 0.001 TYR A 495 ARG 0.009 0.001 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 54) link_NAG-ASN : angle 2.83706 ( 162) link_BETA1-4 : bond 0.00575 ( 14) link_BETA1-4 : angle 2.10178 ( 42) hydrogen bonds : bond 0.22066 ( 954) hydrogen bonds : angle 8.19255 ( 2628) SS BOND : bond 0.00307 ( 37) SS BOND : angle 1.28109 ( 74) covalent geometry : bond 0.00469 (30104) covalent geometry : angle 0.80915 (40961) Misc. bond : bond 0.00014 ( 1) *********************** 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 : 3.308 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: 0.8575 (t0) REVERT: A 487 ASN cc_start: 0.3613 (OUTLIER) cc_final: 0.2392 (t0) REVERT: A 984 LEU cc_start: 0.7962 (tp) cc_final: 0.7711 (tp) 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: 0.3856 time to fit residues: 194.2039 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 : 3.012 ------------------------------------------------------------------------------- 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 305 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 172 optimal weight: 0.5980 chunk 211 optimal weight: 3.9990 chunk 328 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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 B 935 GLN 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 C1005 GLN ** 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 92 ASN E 32 ASN E 92 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.180115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135501 restraints weight = 48993.203| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.36 r_work: 0.3527 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30210 Z= 0.129 Angle : 0.661 17.413 41239 Z= 0.326 Chirality : 0.048 0.749 4798 Planarity : 0.005 0.079 5201 Dihedral : 11.098 107.094 5353 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.31 % Favored : 92.52 % Rotamer: Outliers : 3.17 % Allowed : 23.45 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3611 helix: 1.04 (0.20), residues: 707 sheet: -0.56 (0.18), residues: 846 loop : -2.10 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 633 HIS 0.004 0.001 HIS D 35 PHE 0.016 0.001 PHE A 133 TYR 0.022 0.001 TYR B1067 ARG 0.008 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 54) link_NAG-ASN : angle 2.50764 ( 162) link_BETA1-4 : bond 0.00713 ( 14) link_BETA1-4 : angle 2.69934 ( 42) hydrogen bonds : bond 0.04763 ( 954) hydrogen bonds : angle 5.73996 ( 2628) SS BOND : bond 0.00317 ( 37) SS BOND : angle 1.22888 ( 74) covalent geometry : bond 0.00291 (30104) covalent geometry : angle 0.63655 (40961) Misc. bond : bond 0.00051 ( 1) *********************** 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 394 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 294 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6012 (m-10) REVERT: B 934 ILE cc_start: 0.8842 (tt) cc_final: 0.8505 (tp) REVERT: B 1141 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6681 (mp) REVERT: C 129 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6728 (tttt) REVERT: C 135 PHE cc_start: 0.6630 (t80) cc_final: 0.6216 (t80) REVERT: C 726 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9149 (mm) REVERT: C 940 SER cc_start: 0.8584 (m) cc_final: 0.8182 (p) REVERT: C 1039 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8374 (mtp180) REVERT: C 1106 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: A 242 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 269 TYR cc_start: 0.8688 (m-80) cc_final: 0.8193 (m-80) REVERT: A 487 ASN cc_start: 0.3004 (OUTLIER) cc_final: 0.2092 (t0) REVERT: A 492 LEU cc_start: 0.1337 (OUTLIER) cc_final: 0.0910 (tp) REVERT: A 619 GLU cc_start: 0.7863 (tt0) cc_final: 0.7595 (tt0) REVERT: L 11 LEU cc_start: 0.6657 (tp) cc_final: 0.6212 (mp) REVERT: E 54 ARG cc_start: 0.7173 (ttm110) cc_final: 0.6971 (ttm110) outliers start: 100 outliers final: 43 residues processed: 371 average time/residue: 0.4119 time to fit residues: 256.5085 Evaluate side-chains 308 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 3.058 ------------------------------------------------------------------------------- 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 197 ILE 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 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER 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 95 THR Chi-restraints excluded: chain C residue 129 LYS 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 383 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1106 GLN 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 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 492 LEU 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 666 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 1.9990 chunk 355 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 31 optimal weight: 0.0470 chunk 129 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS B 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN A 87 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.170929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.124080 restraints weight = 48902.639| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.19 r_work: 0.3324 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30210 Z= 0.214 Angle : 0.732 17.089 41239 Z= 0.368 Chirality : 0.050 0.688 4798 Planarity : 0.005 0.072 5201 Dihedral : 7.545 108.061 5342 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.00 % Favored : 90.86 % Rotamer: Outliers : 5.26 % Allowed : 23.33 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3611 helix: 0.87 (0.20), residues: 700 sheet: -0.64 (0.17), residues: 923 loop : -2.18 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 633 HIS 0.011 0.001 HIS B 625 PHE 0.043 0.002 PHE A 135 TYR 0.022 0.002 TYR E 91 ARG 0.007 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 54) link_NAG-ASN : angle 2.69818 ( 162) link_BETA1-4 : bond 0.00426 ( 14) link_BETA1-4 : angle 2.33884 ( 42) hydrogen bonds : bond 0.06787 ( 954) hydrogen bonds : angle 5.55992 ( 2628) SS BOND : bond 0.00373 ( 37) SS BOND : angle 1.35768 ( 74) covalent geometry : bond 0.00519 (30104) covalent geometry : angle 0.70812 (40961) Misc. bond : bond 0.00039 ( 1) *********************** 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 443 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 277 time to evaluate : 3.328 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 205 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8379 (t) REVERT: B 329 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6135 (m-10) REVERT: B 1141 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6687 (mp) REVERT: C 135 PHE cc_start: 0.6923 (t80) cc_final: 0.6386 (t80) REVERT: C 200 TYR cc_start: 0.7472 (m-80) cc_final: 0.7196 (m-80) REVERT: C 571 ASP cc_start: 0.7866 (m-30) cc_final: 0.7582 (p0) REVERT: C 759 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7059 (t80) REVERT: C 778 THR cc_start: 0.9204 (t) cc_final: 0.8966 (m) REVERT: C 940 SER cc_start: 0.8630 (m) cc_final: 0.8192 (p) REVERT: C 1039 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8827 (ptm160) REVERT: A 40 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8268 (p0) REVERT: A 238 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 242 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7248 (mm) REVERT: A 265 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.6842 (m-80) REVERT: A 487 ASN cc_start: 0.2355 (OUTLIER) cc_final: 0.1723 (t0) REVERT: A 619 GLU cc_start: 0.8174 (tt0) cc_final: 0.7966 (tt0) REVERT: A 775 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: H 106 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7975 (p90) REVERT: L 54 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7853 (mtm110) REVERT: D 16 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.7999 (mtm110) REVERT: D 73 ASP cc_start: 0.8790 (t0) cc_final: 0.8379 (t0) REVERT: D 76 LYS cc_start: 0.9252 (mtpt) cc_final: 0.8761 (mtpp) REVERT: D 83 MET cc_start: 0.8330 (mtm) cc_final: 0.8029 (mtm) REVERT: D 101 PRO cc_start: 0.8863 (Cg_exo) cc_final: 0.8660 (Cg_endo) REVERT: D 106 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7233 (p90) REVERT: E 4 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.4313 (mpt) outliers start: 166 outliers final: 84 residues processed: 407 average time/residue: 0.3792 time to fit residues: 255.2037 Evaluate side-chains 330 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 231 time to evaluate : 3.231 ------------------------------------------------------------------------------- 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 205 SER Chi-restraints excluded: chain B residue 238 PHE 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 495 TYR 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 604 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 720 ILE 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 1122 VAL Chi-restraints excluded: chain B residue 1137 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 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 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 569 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 40 ASP 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 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR 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 894 LEU 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 104 SER Chi-restraints excluded: chain H residue 106 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 ARG 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 27 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 95 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 269 optimal weight: 0.5980 chunk 156 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 308 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 506 GLN B 762 GLN B 901 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 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** D 35 HIS E 32 ASN E 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.169124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120602 restraints weight = 48988.023| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.71 r_work: 0.3343 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30210 Z= 0.164 Angle : 0.653 17.096 41239 Z= 0.328 Chirality : 0.047 0.690 4798 Planarity : 0.005 0.086 5201 Dihedral : 6.826 100.167 5341 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.64 % Favored : 92.22 % Rotamer: Outliers : 4.88 % Allowed : 24.06 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3611 helix: 1.15 (0.20), residues: 700 sheet: -0.58 (0.17), residues: 904 loop : -2.13 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 353 HIS 0.015 0.001 HIS B 625 PHE 0.017 0.001 PHE B 329 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 54) link_NAG-ASN : angle 2.61426 ( 162) link_BETA1-4 : bond 0.00433 ( 14) link_BETA1-4 : angle 2.13270 ( 42) hydrogen bonds : bond 0.05419 ( 954) hydrogen bonds : angle 5.24608 ( 2628) SS BOND : bond 0.00459 ( 37) SS BOND : angle 1.34863 ( 74) covalent geometry : bond 0.00390 (30104) covalent geometry : angle 0.62757 (40961) Misc. bond : bond 0.00037 ( 1) *********************** 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 420 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 266 time to evaluate : 3.094 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: 0.8634 (OUTLIER) cc_final: 0.8383 (t) REVERT: B 179 LEU cc_start: 0.4808 (OUTLIER) cc_final: 0.4506 (pp) REVERT: B 327 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7919 (t) REVERT: B 329 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6194 (m-10) REVERT: B 1141 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6456 (mp) REVERT: C 129 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7043 (mtpt) REVERT: C 135 PHE cc_start: 0.6900 (t80) cc_final: 0.6307 (t80) REVERT: C 200 TYR cc_start: 0.7363 (m-80) cc_final: 0.7104 (m-80) REVERT: C 238 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7788 (t80) REVERT: C 759 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7124 (t80) REVERT: C 778 THR cc_start: 0.9041 (t) cc_final: 0.8837 (m) REVERT: C 779 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: C 940 SER cc_start: 0.8555 (m) cc_final: 0.8061 (p) REVERT: A 238 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7944 (t80) REVERT: A 242 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7356 (mm) REVERT: A 265 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6788 (m-80) REVERT: A 487 ASN cc_start: 0.2664 (OUTLIER) cc_final: 0.1931 (t0) REVERT: A 775 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: H 106 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7654 (p90) REVERT: L 54 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8068 (mtm110) REVERT: D 34 MET cc_start: 0.8807 (mmm) cc_final: 0.8607 (mmt) REVERT: D 106 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7111 (p90) REVERT: E 4 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.4630 (mpt) REVERT: E 38 GLN cc_start: 0.5096 (tp40) cc_final: 0.4425 (tt0) outliers start: 154 outliers final: 80 residues processed: 388 average time/residue: 0.3693 time to fit residues: 238.2318 Evaluate side-chains 337 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 240 time to evaluate : 3.136 ------------------------------------------------------------------------------- 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 80 ASP 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 274 THR Chi-restraints excluded: chain B residue 287 ASP 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 562 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET 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 41 LYS Chi-restraints excluded: chain C residue 51 THR 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 129 LYS 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 240 THR Chi-restraints excluded: chain C residue 302 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 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 959 LEU 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 A residue 47 VAL 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 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 487 ASN Chi-restraints excluded: chain A residue 597 VAL 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 916 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 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 L residue 97 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 255 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 271 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 323 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 762 GLN B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** 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 762 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.171100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.122975 restraints weight = 48663.417| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.66 r_work: 0.3368 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30210 Z= 0.126 Angle : 0.615 16.437 41239 Z= 0.307 Chirality : 0.046 0.674 4798 Planarity : 0.004 0.076 5201 Dihedral : 6.307 91.489 5341 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.00 % Favored : 91.86 % Rotamer: Outliers : 4.63 % Allowed : 24.22 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3611 helix: 1.36 (0.20), residues: 700 sheet: -0.54 (0.18), residues: 892 loop : -2.06 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.006 0.001 HIS B 625 PHE 0.015 0.001 PHE B 329 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 54) link_NAG-ASN : angle 2.44952 ( 162) link_BETA1-4 : bond 0.00581 ( 14) link_BETA1-4 : angle 1.95492 ( 42) hydrogen bonds : bond 0.04782 ( 954) hydrogen bonds : angle 5.06047 ( 2628) SS BOND : bond 0.00481 ( 37) SS BOND : angle 1.36333 ( 74) covalent geometry : bond 0.00290 (30104) covalent geometry : angle 0.59133 (40961) Misc. bond : bond 0.00041 ( 1) *********************** 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 407 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 261 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8359 (t) REVERT: B 41 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7192 (mttp) REVERT: B 179 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4623 (pp) REVERT: B 246 ARG cc_start: 0.5138 (OUTLIER) cc_final: 0.3528 (mmm160) REVERT: B 327 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.7912 (t) REVERT: B 329 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6015 (m-10) REVERT: B 754 LEU cc_start: 0.9050 (tp) cc_final: 0.8809 (tt) REVERT: B 1141 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6350 (mp) REVERT: C 135 PHE cc_start: 0.6929 (t80) cc_final: 0.6225 (t80) REVERT: C 238 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.7957 (t80) REVERT: C 489 TYR cc_start: 0.2090 (OUTLIER) cc_final: 0.0999 (m-80) REVERT: C 529 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8534 (ttmm) REVERT: C 778 THR cc_start: 0.8943 (t) cc_final: 0.8715 (m) REVERT: C 779 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: C 983 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7995 (mtm110) REVERT: A 66 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7293 (t-90) REVERT: A 242 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7390 (mm) REVERT: A 265 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: A 269 TYR cc_start: 0.8769 (m-80) cc_final: 0.8419 (m-80) REVERT: A 487 ASN cc_start: 0.2813 (OUTLIER) cc_final: 0.2145 (t0) REVERT: A 775 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: A 984 LEU cc_start: 0.8089 (mm) cc_final: 0.7784 (mp) REVERT: H 106 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7642 (p90) REVERT: L 54 ARG cc_start: 0.8383 (mtm110) cc_final: 0.8025 (mtm110) REVERT: D 16 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.7962 (mtm110) REVERT: D 106 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7263 (p90) REVERT: E 4 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.4702 (mpt) outliers start: 146 outliers final: 79 residues processed: 377 average time/residue: 0.5501 time to fit residues: 347.5290 Evaluate side-chains 332 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 235 time to evaluate : 4.518 ------------------------------------------------------------------------------- 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 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 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 620 VAL Chi-restraints excluded: chain B residue 641 ASN 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 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 51 THR 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 229 LEU Chi-restraints excluded: chain C residue 238 PHE 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 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 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 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 319 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL 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 867 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL 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 L residue 97 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 12 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 217 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** 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 32 ASN E 42 GLN E 92 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.169528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122322 restraints weight = 48779.491| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.97 r_work: 0.3282 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30210 Z= 0.208 Angle : 0.696 16.657 41239 Z= 0.349 Chirality : 0.048 0.680 4798 Planarity : 0.005 0.068 5201 Dihedral : 6.394 87.901 5341 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.06 % Favored : 90.81 % Rotamer: Outliers : 5.26 % Allowed : 23.87 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3611 helix: 1.19 (0.20), residues: 691 sheet: -0.60 (0.17), residues: 892 loop : -2.14 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 35 HIS 0.010 0.001 HIS B 625 PHE 0.020 0.002 PHE C 86 TYR 0.019 0.002 TYR A1067 ARG 0.008 0.001 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 54) link_NAG-ASN : angle 2.69588 ( 162) link_BETA1-4 : bond 0.00438 ( 14) link_BETA1-4 : angle 1.95105 ( 42) hydrogen bonds : bond 0.06193 ( 954) hydrogen bonds : angle 5.28846 ( 2628) SS BOND : bond 0.00442 ( 37) SS BOND : angle 1.84505 ( 74) covalent geometry : bond 0.00509 (30104) covalent geometry : angle 0.67018 (40961) Misc. bond : bond 0.00036 ( 1) *********************** 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 413 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 247 time to evaluate : 3.629 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 41 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7351 (mttp) REVERT: B 135 PHE cc_start: 0.7271 (p90) cc_final: 0.6254 (t80) REVERT: B 179 LEU cc_start: 0.4633 (OUTLIER) cc_final: 0.4300 (pp) REVERT: B 237 ARG cc_start: 0.5401 (mtt180) cc_final: 0.5087 (ptp-110) REVERT: B 246 ARG cc_start: 0.4975 (OUTLIER) cc_final: 0.3185 (mmm160) REVERT: B 329 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6293 (m-10) REVERT: B 754 LEU cc_start: 0.9097 (tp) cc_final: 0.8863 (tt) REVERT: C 238 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7831 (t80) REVERT: C 489 TYR cc_start: 0.2340 (OUTLIER) cc_final: 0.1272 (m-80) REVERT: C 529 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8567 (ttmm) REVERT: C 759 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7482 (t80) REVERT: C 778 THR cc_start: 0.9162 (t) cc_final: 0.8927 (m) REVERT: A 66 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7504 (t-90) REVERT: A 242 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7580 (mm) REVERT: A 265 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: A 487 ASN cc_start: 0.2801 (OUTLIER) cc_final: 0.2066 (t0) REVERT: A 656 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8450 (m) REVERT: A 775 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: A 984 LEU cc_start: 0.8169 (mm) cc_final: 0.7896 (mp) REVERT: H 106 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7604 (p90) REVERT: L 54 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8010 (mtm110) REVERT: D 73 ASP cc_start: 0.8774 (t0) cc_final: 0.8346 (t0) REVERT: D 83 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7857 (mtm) REVERT: D 106 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7388 (p90) REVERT: E 4 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5585 (mmm) outliers start: 166 outliers final: 105 residues processed: 378 average time/residue: 0.3901 time to fit residues: 248.0188 Evaluate side-chains 359 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 236 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 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 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 317 ASN 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 495 TYR 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 604 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 641 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET 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 1100 THR 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 51 THR 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 302 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 382 VAL 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 565 PHE 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 759 PHE Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 911 VAL 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 C residue 1136 THR 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 179 LEU 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 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 319 ARG Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL 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 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 106 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 54 ARG 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 D residue 75 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 ASN 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 193 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 179 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 292 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.171313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127040 restraints weight = 49200.982| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.73 r_work: 0.3339 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30210 Z= 0.117 Angle : 0.623 15.978 41239 Z= 0.311 Chirality : 0.046 0.660 4798 Planarity : 0.004 0.063 5201 Dihedral : 6.065 87.619 5341 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.64 % Favored : 92.22 % Rotamer: Outliers : 3.71 % Allowed : 25.29 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3611 helix: 1.41 (0.21), residues: 695 sheet: -0.49 (0.18), residues: 884 loop : -2.06 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 436 HIS 0.017 0.001 HIS B 625 PHE 0.014 0.001 PHE B 329 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 54) link_NAG-ASN : angle 2.42442 ( 162) link_BETA1-4 : bond 0.00535 ( 14) link_BETA1-4 : angle 1.84436 ( 42) hydrogen bonds : bond 0.04732 ( 954) hydrogen bonds : angle 5.02994 ( 2628) SS BOND : bond 0.00317 ( 37) SS BOND : angle 1.53030 ( 74) covalent geometry : bond 0.00265 (30104) covalent geometry : angle 0.60018 (40961) Misc. bond : bond 0.00044 ( 1) *********************** 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 373 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 256 time to evaluate : 2.983 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 41 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7397 (mttm) REVERT: B 135 PHE cc_start: 0.7155 (p90) cc_final: 0.6220 (t80) REVERT: B 179 LEU cc_start: 0.4743 (OUTLIER) cc_final: 0.4389 (pp) REVERT: B 237 ARG cc_start: 0.5498 (mtt180) cc_final: 0.5145 (ptp-110) REVERT: B 246 ARG cc_start: 0.5116 (OUTLIER) cc_final: 0.3360 (mmm160) REVERT: B 327 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8024 (t) REVERT: B 329 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6225 (m-10) REVERT: B 616 ASN cc_start: 0.7441 (t0) cc_final: 0.6657 (p0) REVERT: B 754 LEU cc_start: 0.9097 (tp) cc_final: 0.8877 (tt) REVERT: C 135 PHE cc_start: 0.7033 (t80) cc_final: 0.6223 (t80) REVERT: C 238 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7997 (t80) REVERT: C 489 TYR cc_start: 0.2569 (OUTLIER) cc_final: 0.1261 (m-80) REVERT: C 529 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8552 (ttmm) REVERT: C 778 THR cc_start: 0.8880 (t) cc_final: 0.8667 (m) REVERT: C 918 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: A 66 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7521 (t-90) REVERT: A 242 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7673 (mm) REVERT: A 265 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: A 269 TYR cc_start: 0.8772 (m-80) cc_final: 0.8411 (m-80) REVERT: A 487 ASN cc_start: 0.3216 (OUTLIER) cc_final: 0.2368 (t0) REVERT: A 775 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: A 984 LEU cc_start: 0.8115 (mm) cc_final: 0.7862 (mp) REVERT: H 106 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7537 (p90) REVERT: L 54 ARG cc_start: 0.8333 (mtm110) cc_final: 0.7944 (mtm110) REVERT: D 73 ASP cc_start: 0.8711 (t0) cc_final: 0.8330 (t0) REVERT: D 76 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8748 (mtpp) REVERT: D 83 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7789 (mtm) REVERT: D 106 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7592 (p90) REVERT: E 4 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.5775 (mmm) outliers start: 117 outliers final: 81 residues processed: 348 average time/residue: 0.4175 time to fit residues: 242.4612 Evaluate side-chains 332 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 234 time to evaluate : 3.394 ------------------------------------------------------------------------------- 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 62 VAL 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 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 495 TYR 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 604 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 931 ILE 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 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 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 660 TYR Chi-restraints excluded: chain C residue 784 GLN 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 1122 VAL Chi-restraints excluded: chain C residue 1136 THR 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 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 319 ARG Chi-restraints excluded: chain A residue 392 PHE 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 625 HIS 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 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 1122 VAL 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 42 GLN 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 D residue 83 MET Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 141 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 65 optimal weight: 0.0670 chunk 286 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 355 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 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 239 GLN ** A 334 ASN ** 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 79 GLN L 89 GLN E 32 ASN E 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.167435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119558 restraints weight = 48741.856| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.69 r_work: 0.3283 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30210 Z= 0.225 Angle : 0.695 16.396 41239 Z= 0.350 Chirality : 0.048 0.672 4798 Planarity : 0.005 0.066 5201 Dihedral : 6.308 87.308 5341 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.39 % Favored : 90.47 % Rotamer: Outliers : 4.44 % Allowed : 24.82 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3611 helix: 1.28 (0.20), residues: 693 sheet: -0.50 (0.17), residues: 881 loop : -2.18 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 35 HIS 0.008 0.001 HIS B 625 PHE 0.020 0.002 PHE C 86 TYR 0.020 0.002 TYR A1067 ARG 0.008 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 54) link_NAG-ASN : angle 2.57500 ( 162) link_BETA1-4 : bond 0.00439 ( 14) link_BETA1-4 : angle 1.90363 ( 42) hydrogen bonds : bond 0.06108 ( 954) hydrogen bonds : angle 5.24798 ( 2628) SS BOND : bond 0.00375 ( 37) SS BOND : angle 1.72723 ( 74) covalent geometry : bond 0.00554 (30104) covalent geometry : angle 0.67158 (40961) Misc. bond : bond 0.00037 ( 1) *********************** 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 383 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 243 time to evaluate : 3.157 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 41 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7434 (mttp) REVERT: B 135 PHE cc_start: 0.7301 (p90) cc_final: 0.6394 (t80) REVERT: B 179 LEU cc_start: 0.4583 (OUTLIER) cc_final: 0.4223 (pp) REVERT: B 200 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: B 237 ARG cc_start: 0.5739 (mtt180) cc_final: 0.5397 (ptp-110) REVERT: B 246 ARG cc_start: 0.5086 (OUTLIER) cc_final: 0.3234 (mmm160) REVERT: B 327 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.7937 (t) REVERT: B 329 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6313 (m-10) REVERT: B 616 ASN cc_start: 0.7548 (t0) cc_final: 0.6705 (p0) REVERT: B 625 HIS cc_start: 0.7536 (t70) cc_final: 0.7127 (m170) REVERT: B 754 LEU cc_start: 0.9108 (tp) cc_final: 0.8885 (tt) REVERT: C 238 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.7879 (t80) REVERT: C 489 TYR cc_start: 0.2176 (OUTLIER) cc_final: 0.1131 (m-80) REVERT: C 529 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8573 (ttmm) REVERT: C 778 THR cc_start: 0.9171 (t) cc_final: 0.8943 (m) REVERT: A 66 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7505 (t-90) REVERT: A 242 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7535 (mm) REVERT: A 265 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: A 487 ASN cc_start: 0.2760 (OUTLIER) cc_final: 0.2249 (t0) REVERT: A 656 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8498 (m) REVERT: A 775 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: A 816 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8815 (m) REVERT: A 984 LEU cc_start: 0.8208 (mm) cc_final: 0.7978 (mp) REVERT: H 106 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7552 (p90) REVERT: L 54 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8009 (mtm110) REVERT: D 76 LYS cc_start: 0.9277 (mtpt) cc_final: 0.8988 (mtpp) REVERT: D 106 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7442 (p90) REVERT: E 4 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5595 (mmm) outliers start: 140 outliers final: 102 residues processed: 353 average time/residue: 0.3998 time to fit residues: 233.4099 Evaluate side-chains 353 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 233 time to evaluate : 3.441 ------------------------------------------------------------------------------- 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 200 TYR 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 495 TYR 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 604 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 931 ILE 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 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 51 THR 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 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 565 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 784 GLN 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 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER 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 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 392 PHE 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 597 VAL Chi-restraints excluded: chain A residue 656 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 816 SER 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 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 5 THR 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 L residue 58 ILE 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 D residue 75 SER Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 240 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** 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 32 ASN E 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.171532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126769 restraints weight = 48816.607| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 4.41 r_work: 0.3322 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30210 Z= 0.123 Angle : 0.631 15.800 41239 Z= 0.315 Chirality : 0.046 0.650 4798 Planarity : 0.004 0.061 5201 Dihedral : 5.972 85.760 5341 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.34 % Favored : 92.52 % Rotamer: Outliers : 3.87 % Allowed : 25.55 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3611 helix: 1.46 (0.21), residues: 695 sheet: -0.43 (0.18), residues: 885 loop : -2.06 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.003 0.001 HIS D 35 PHE 0.015 0.001 PHE C 135 TYR 0.018 0.001 TYR B1067 ARG 0.008 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 54) link_NAG-ASN : angle 2.42782 ( 162) link_BETA1-4 : bond 0.00529 ( 14) link_BETA1-4 : angle 1.81107 ( 42) hydrogen bonds : bond 0.04731 ( 954) hydrogen bonds : angle 5.01757 ( 2628) SS BOND : bond 0.00307 ( 37) SS BOND : angle 1.43040 ( 74) covalent geometry : bond 0.00282 (30104) covalent geometry : angle 0.60818 (40961) Misc. bond : bond 0.00042 ( 1) *********************** 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 361 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 239 time to evaluate : 3.394 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: 0.7678 (OUTLIER) cc_final: 0.7466 (mttm) REVERT: B 135 PHE cc_start: 0.7267 (p90) cc_final: 0.6453 (t80) REVERT: B 179 LEU cc_start: 0.4607 (OUTLIER) cc_final: 0.4222 (pp) REVERT: B 246 ARG cc_start: 0.5082 (OUTLIER) cc_final: 0.3363 (mmm160) REVERT: B 327 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.7850 (t) REVERT: B 329 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6207 (m-10) REVERT: B 625 HIS cc_start: 0.7561 (t70) cc_final: 0.7249 (m170) REVERT: B 754 LEU cc_start: 0.9109 (tp) cc_final: 0.8897 (tt) REVERT: C 135 PHE cc_start: 0.7190 (t80) cc_final: 0.6548 (t80) REVERT: C 238 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8029 (t80) REVERT: C 489 TYR cc_start: 0.2129 (OUTLIER) cc_final: 0.1123 (m-80) REVERT: C 529 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8599 (ttmm) REVERT: C 577 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6469 (ptm160) REVERT: C 759 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7355 (t80) REVERT: C 778 THR cc_start: 0.8886 (t) cc_final: 0.8680 (m) REVERT: C 918 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: A 40 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8248 (p0) REVERT: A 66 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7464 (t-90) REVERT: A 242 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 265 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: A 269 TYR cc_start: 0.8796 (m-80) cc_final: 0.8397 (m-80) REVERT: A 487 ASN cc_start: 0.2618 (OUTLIER) cc_final: 0.2102 (t0) REVERT: A 656 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8473 (m) REVERT: A 775 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: A 816 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8835 (m) REVERT: A 984 LEU cc_start: 0.8149 (mm) cc_final: 0.7943 (mp) REVERT: H 106 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.7612 (p90) REVERT: L 54 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8073 (mtm110) REVERT: D 76 LYS cc_start: 0.9229 (mtpt) cc_final: 0.8954 (mtpp) REVERT: D 83 MET cc_start: 0.8264 (mtm) cc_final: 0.7897 (mtm) REVERT: D 106 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7535 (p90) REVERT: E 4 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.5772 (mmm) REVERT: E 38 GLN cc_start: 0.4997 (OUTLIER) cc_final: 0.4306 (tt0) REVERT: E 71 PHE cc_start: 0.7942 (m-80) cc_final: 0.7650 (m-80) outliers start: 122 outliers final: 85 residues processed: 337 average time/residue: 0.3932 time to fit residues: 218.2430 Evaluate side-chains 340 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 233 time to evaluate : 2.956 ------------------------------------------------------------------------------- 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 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 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 495 TYR 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 604 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL 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 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 302 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 565 PHE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 994 ASP 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 392 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL 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 816 SER 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 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 H residue 109 PHE Chi-restraints excluded: chain L residue 42 GLN 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 D residue 106 PHE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 185 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 0.0270 chunk 348 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 71 optimal weight: 0.1980 overall best weight: 1.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 613 GLN ** 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 334 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.169548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122478 restraints weight = 48577.103| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 4.03 r_work: 0.3304 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30210 Z= 0.162 Angle : 0.652 15.864 41239 Z= 0.326 Chirality : 0.047 0.656 4798 Planarity : 0.005 0.058 5201 Dihedral : 5.985 86.188 5341 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.45 % Favored : 91.42 % Rotamer: Outliers : 3.74 % Allowed : 25.45 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3611 helix: 1.42 (0.21), residues: 695 sheet: -0.39 (0.18), residues: 873 loop : -2.09 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 35 HIS 0.003 0.001 HIS C1048 PHE 0.025 0.001 PHE A 86 TYR 0.019 0.001 TYR A1067 ARG 0.023 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 54) link_NAG-ASN : angle 2.43862 ( 162) link_BETA1-4 : bond 0.00459 ( 14) link_BETA1-4 : angle 1.82255 ( 42) hydrogen bonds : bond 0.05240 ( 954) hydrogen bonds : angle 5.04225 ( 2628) SS BOND : bond 0.00322 ( 37) SS BOND : angle 1.61180 ( 74) covalent geometry : bond 0.00393 (30104) covalent geometry : angle 0.62996 (40961) Misc. bond : bond 0.00035 ( 1) ********************** 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 356 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 238 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7575 (mttm) REVERT: B 135 PHE cc_start: 0.7337 (p90) cc_final: 0.6498 (t80) REVERT: B 179 LEU cc_start: 0.4415 (OUTLIER) cc_final: 0.4063 (pp) REVERT: B 246 ARG cc_start: 0.5068 (OUTLIER) cc_final: 0.3308 (mmm160) REVERT: B 327 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8146 (t) REVERT: B 616 ASN cc_start: 0.7344 (t0) cc_final: 0.6666 (p0) REVERT: B 625 HIS cc_start: 0.7465 (t70) cc_final: 0.7236 (m170) REVERT: B 754 LEU cc_start: 0.9113 (tp) cc_final: 0.8897 (tt) REVERT: C 135 PHE cc_start: 0.7324 (t80) cc_final: 0.6667 (t80) REVERT: C 238 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.7830 (t80) REVERT: C 489 TYR cc_start: 0.2195 (OUTLIER) cc_final: 0.1141 (m-80) REVERT: C 529 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8593 (ttmm) REVERT: C 577 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6419 (ptm160) REVERT: C 661 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8187 (pm20) REVERT: C 759 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7445 (t80) REVERT: C 778 THR cc_start: 0.8985 (t) cc_final: 0.8769 (m) REVERT: C 878 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8876 (tt) REVERT: C 918 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: A 40 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8231 (p0) REVERT: A 66 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7504 (t-90) REVERT: A 242 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7442 (mm) REVERT: A 265 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: A 487 ASN cc_start: 0.2733 (OUTLIER) cc_final: 0.2156 (t0) REVERT: A 656 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8458 (m) REVERT: A 775 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: A 816 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.8842 (m) REVERT: H 106 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7564 (p90) REVERT: L 54 ARG cc_start: 0.8440 (mtm110) cc_final: 0.8097 (mtm110) REVERT: D 76 LYS cc_start: 0.9248 (mtpt) cc_final: 0.8968 (mtpp) REVERT: D 83 MET cc_start: 0.8316 (mtm) cc_final: 0.7913 (mtm) REVERT: D 106 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7606 (p90) REVERT: E 4 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5761 (mmm) REVERT: E 27 GLN cc_start: 0.6614 (mt0) cc_final: 0.6124 (tm-30) REVERT: E 38 GLN cc_start: 0.5128 (OUTLIER) cc_final: 0.4181 (tt0) REVERT: E 71 PHE cc_start: 0.7905 (m-80) cc_final: 0.7587 (m-80) outliers start: 118 outliers final: 89 residues processed: 332 average time/residue: 0.3850 time to fit residues: 211.1788 Evaluate side-chains 342 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 231 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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 62 VAL 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 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 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 495 TYR 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 604 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL 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 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 302 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 565 PHE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 918 GLU 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 179 LEU 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 229 LEU 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 392 PHE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 656 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 816 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 106 PHE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 42 GLN 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 D residue 106 PHE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 38 GLN 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 320 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** 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 334 ASN ** 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 37 HIS D 1 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.168291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121967 restraints weight = 49044.833| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.75 r_work: 0.3284 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30210 Z= 0.195 Angle : 0.684 15.852 41239 Z= 0.343 Chirality : 0.048 0.656 4798 Planarity : 0.005 0.064 5201 Dihedral : 6.168 88.469 5341 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.06 % Favored : 90.83 % Rotamer: Outliers : 4.09 % Allowed : 25.26 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3611 helix: 1.33 (0.21), residues: 695 sheet: -0.47 (0.17), residues: 905 loop : -2.17 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 436 HIS 0.005 0.001 HIS C1048 PHE 0.032 0.002 PHE A 375 TYR 0.024 0.002 TYR A 508 ARG 0.009 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 54) link_NAG-ASN : angle 2.50795 ( 162) link_BETA1-4 : bond 0.00437 ( 14) link_BETA1-4 : angle 1.83144 ( 42) hydrogen bonds : bond 0.05802 ( 954) hydrogen bonds : angle 5.17580 ( 2628) SS BOND : bond 0.00353 ( 37) SS BOND : angle 1.75656 ( 74) covalent geometry : bond 0.00476 (30104) covalent geometry : angle 0.66157 (40961) Misc. bond : bond 0.00034 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15702.38 seconds wall clock time: 276 minutes 43.50 seconds (16603.50 seconds total)