Starting phenix.real_space_refine on Tue Aug 26 22:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jal_6350/08_2025/3jal_6350.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jal_6350/08_2025/3jal_6350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jal_6350/08_2025/3jal_6350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jal_6350/08_2025/3jal_6350.map" model { file = "/net/cci-nas-00/data/ceres_data/3jal_6350/08_2025/3jal_6350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jal_6350/08_2025/3jal_6350.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.010 sd= 0.921 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 290 5.16 5 C 27078 2.51 5 N 7340 2.21 5 O 8268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43012 Number of models: 1 Model: "" Number of chains: 26 Chain: "E" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 7.35, per 1000 atoms: 0.17 Number of scatterers: 43012 At special positions: 0 Unit cell: (172.92, 112.2, 212.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 290 16.00 P 30 15.00 Mg 6 11.99 O 8268 8.00 N 7340 7.00 C 27078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10080 Finding SS restraints... Secondary structure from input PDB file: 268 helices and 30 sheets defined 56.1% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.624A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.633A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.617A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.080A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 205 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.481A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.556A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.984A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 298 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.220A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.931A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.909A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.521A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.749A pdb=" N PHE F 87 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.633A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.764A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 3.684A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 297 through 301 removed outlier: 3.622A pdb=" N ASN F 300 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 400 Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.086A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 438 removed outlier: 3.665A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 29 Processing helix chain 'N' and resid 34 through 40 removed outlier: 3.562A pdb=" N SER N 40 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 52 Processing helix chain 'N' and resid 57 through 61 Processing helix chain 'N' and resid 67 through 86 Processing helix chain 'N' and resid 92 through 98 removed outlier: 3.863A pdb=" N LYS N 98 " --> pdb=" O GLU N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 119 Processing helix chain 'N' and resid 125 through 131 removed outlier: 4.001A pdb=" N ALA N 129 " --> pdb=" O ASN N 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 48 through 51 removed outlier: 3.624A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 48 through 51' Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.634A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.621A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.083A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 205 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.478A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.554A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 removed outlier: 3.985A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 298 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 Processing helix chain 'J' and resid 383 through 400 removed outlier: 4.220A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 3.926A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.910A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.520A pdb=" N ARG G 48 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 72 through 81 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.750A pdb=" N PHE G 87 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 129 removed outlier: 4.633A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.763A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 3.684A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 297 through 301 removed outlier: 3.623A pdb=" N ASN G 300 " --> pdb=" O ASP G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 384 through 400 Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.087A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 438 removed outlier: 3.665A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.624A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.632A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.617A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.081A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.482A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.556A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.985A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 400 removed outlier: 4.220A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.931A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.909A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.521A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.750A pdb=" N PHE D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.633A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.763A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.683A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.621A pdb=" N ASN D 300 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.086A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 438 removed outlier: 3.666A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 48 through 51 removed outlier: 3.624A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.632A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.617A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.080A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 205 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.481A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 3.555A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 282 removed outlier: 3.986A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 298 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 Processing helix chain 'L' and resid 383 through 400 removed outlier: 4.220A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 3.930A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.909A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.519A pdb=" N ARG I 48 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 72 through 81 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.750A pdb=" N PHE I 87 " --> pdb=" O GLY I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 109 through 129 removed outlier: 4.633A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.764A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.682A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 287 through 296 Processing helix chain 'I' and resid 297 through 301 removed outlier: 3.622A pdb=" N ASN I 300 " --> pdb=" O ASP I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 339 Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 384 through 400 Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.086A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 438 removed outlier: 3.665A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.624A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.632A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.617A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.082A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.480A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.556A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.984A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.220A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.930A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.909A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.520A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.749A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.633A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.763A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.683A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.621A pdb=" N ASN B 300 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.086A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 438 removed outlier: 3.665A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 29 Processing helix chain 'M' and resid 34 through 40 removed outlier: 3.563A pdb=" N SER M 40 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 52 Processing helix chain 'M' and resid 57 through 61 Processing helix chain 'M' and resid 67 through 86 Processing helix chain 'M' and resid 92 through 98 removed outlier: 3.862A pdb=" N LYS M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 119 Processing helix chain 'M' and resid 125 through 131 removed outlier: 4.002A pdb=" N ALA M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 48 through 51 removed outlier: 3.623A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.632A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.617A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.080A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 196 through 198 No H-bonds generated for 'chain 'K' and resid 196 through 198' Processing helix chain 'K' and resid 205 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.481A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.553A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 282 removed outlier: 3.986A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 298 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 400 removed outlier: 4.220A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 3.929A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.909A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.519A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.750A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.634A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.764A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.684A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 287 through 296 Processing helix chain 'H' and resid 297 through 301 removed outlier: 3.622A pdb=" N ASN H 300 " --> pdb=" O ASP H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 400 Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.087A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 438 removed outlier: 3.665A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.027A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=C, first strand: chain 'E' and resid 246 through 248 removed outlier: 3.596A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.597A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.814A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.028A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=H, first strand: chain 'J' and resid 246 through 248 removed outlier: 3.591A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU G 137 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE G 7 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.597A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.814A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.027A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=M, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.595A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.598A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.814A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.028A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=R, first strand: chain 'L' and resid 246 through 248 removed outlier: 3.594A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU I 137 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE I 7 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.596A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.813A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.027A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=W, first strand: chain 'A' and resid 246 through 248 removed outlier: 3.595A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.598A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.813A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.027A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AB, first strand: chain 'K' and resid 246 through 248 removed outlier: 3.593A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.597A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.813A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) 2206 hydrogen bonds defined for protein. 6408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.86 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7302 1.32 - 1.44: 11914 1.44 - 1.57: 24261 1.57 - 1.69: 55 1.69 - 1.81: 466 Bond restraints: 43998 Sorted by residual: bond pdb=" O3B G2P D 501 " pdb=" PB G2P D 501 " ideal model delta sigma weight residual 1.612 1.477 0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" O3B G2P I 501 " pdb=" PB G2P I 501 " ideal model delta sigma weight residual 1.612 1.478 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" O3B G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 1.612 1.478 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" O3B G2P H 501 " pdb=" PB G2P H 501 " ideal model delta sigma weight residual 1.612 1.479 0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" O3B G2P F 501 " pdb=" PB G2P F 501 " ideal model delta sigma weight residual 1.612 1.479 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 43993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 57336 3.02 - 6.03: 2207 6.03 - 9.05: 134 9.05 - 12.07: 51 12.07 - 15.08: 18 Bond angle restraints: 59746 Sorted by residual: angle pdb=" O VAL G 288 " pdb=" C VAL G 288 " pdb=" N PRO G 289 " ideal model delta sigma weight residual 120.07 124.01 -3.94 7.10e-01 1.98e+00 3.07e+01 angle pdb=" O VAL H 288 " pdb=" C VAL H 288 " pdb=" N PRO H 289 " ideal model delta sigma weight residual 120.07 124.00 -3.93 7.10e-01 1.98e+00 3.06e+01 angle pdb=" O VAL D 288 " pdb=" C VAL D 288 " pdb=" N PRO D 289 " ideal model delta sigma weight residual 120.07 123.97 -3.90 7.10e-01 1.98e+00 3.01e+01 angle pdb=" O VAL F 288 " pdb=" C VAL F 288 " pdb=" N PRO F 289 " ideal model delta sigma weight residual 120.07 123.97 -3.90 7.10e-01 1.98e+00 3.01e+01 angle pdb=" O VAL B 288 " pdb=" C VAL B 288 " pdb=" N PRO B 289 " ideal model delta sigma weight residual 120.07 123.97 -3.90 7.10e-01 1.98e+00 3.01e+01 ... (remaining 59741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 25455 33.88 - 67.76: 749 67.76 - 101.64: 35 101.64 - 135.52: 1 135.52 - 169.40: 18 Dihedral angle restraints: 26258 sinusoidal: 10554 harmonic: 15704 Sorted by residual: dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.33 -169.40 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.56 -169.17 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.58 -169.15 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 26255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4997 0.094 - 0.188: 1283 0.188 - 0.283: 205 0.283 - 0.377: 31 0.377 - 0.471: 6 Chirality restraints: 6522 Sorted by residual: chirality pdb=" C3' G2P I 501 " pdb=" C2' G2P I 501 " pdb=" C4' G2P I 501 " pdb=" O3' G2P I 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.24 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" C3' G2P D 501 " pdb=" C2' G2P D 501 " pdb=" C4' G2P D 501 " pdb=" O3' G2P D 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.24 -0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.24 -0.47 2.00e-01 2.50e+01 5.46e+00 ... (remaining 6519 not shown) Planarity restraints: 7776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA N 117 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ALA N 117 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA N 117 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN N 118 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 88 " -0.037 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO C 89 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 89 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 89 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS L 88 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO L 89 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO L 89 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 89 " -0.032 5.00e-02 4.00e+02 ... (remaining 7773 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 58 2.54 - 3.13: 31713 3.13 - 3.72: 67332 3.72 - 4.31: 96939 4.31 - 4.90: 164894 Nonbonded interactions: 360936 Sorted by model distance: nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.948 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.953 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.959 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.962 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.978 2.170 ... (remaining 360931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'C' selection = chain 'L' selection = chain 'A' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'D' selection = chain 'I' selection = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'N' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.560 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.580 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.120 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.009 0.135 43998 Z= 0.619 Angle : 1.457 15.082 59746 Z= 0.985 Chirality : 0.084 0.471 6522 Planarity : 0.006 0.057 7776 Dihedral : 15.874 169.404 16178 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Rotamer: Outliers : 1.21 % Allowed : 6.65 % Favored : 92.14 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.11), residues: 5388 helix: 0.95 (0.09), residues: 2420 sheet: 0.36 (0.19), residues: 774 loop : -0.89 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 2 TYR 0.019 0.003 TYR I 61 PHE 0.024 0.002 PHE C 351 TRP 0.018 0.003 TRP D 21 HIS 0.012 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00897 (43998) covalent geometry : angle 1.45672 (59746) hydrogen bonds : bond 0.18646 ( 2206) hydrogen bonds : angle 7.16484 ( 6408) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 968 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.8416 (mmm) cc_final: 0.7760 (mmp) REVERT: E 302 MET cc_start: 0.7604 (mtt) cc_final: 0.7363 (mtt) REVERT: E 398 MET cc_start: 0.8428 (mtp) cc_final: 0.8147 (mtm) REVERT: F 278 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8563 (mtm-85) REVERT: F 314 THR cc_start: 0.8795 (p) cc_final: 0.8578 (p) REVERT: N 28 LEU cc_start: 0.8351 (mp) cc_final: 0.8033 (mp) REVERT: N 38 LEU cc_start: 0.8347 (mp) cc_final: 0.8000 (mp) REVERT: N 100 LYS cc_start: 0.5114 (mmtp) cc_final: 0.4640 (ptmt) REVERT: J 124 LYS cc_start: 0.8529 (mttp) cc_final: 0.8329 (mmtt) REVERT: J 154 MET cc_start: 0.8155 (mmm) cc_final: 0.7626 (mmt) REVERT: J 302 MET cc_start: 0.7224 (mtt) cc_final: 0.7018 (mtt) REVERT: J 398 MET cc_start: 0.8666 (mtp) cc_final: 0.8417 (mtm) REVERT: G 59 ASN cc_start: 0.8388 (m110) cc_final: 0.7941 (p0) REVERT: G 97 SER cc_start: 0.8634 (m) cc_final: 0.8384 (p) REVERT: G 314 THR cc_start: 0.8956 (p) cc_final: 0.8517 (p) REVERT: C 253 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8338 (m) REVERT: C 285 GLN cc_start: 0.8320 (pt0) cc_final: 0.7792 (mm110) REVERT: D 166 MET cc_start: 0.8088 (tpp) cc_final: 0.7834 (tpt) REVERT: D 334 ASN cc_start: 0.8326 (t0) cc_final: 0.8093 (t0) REVERT: L 127 ASP cc_start: 0.8408 (m-30) cc_final: 0.8192 (m-30) REVERT: L 154 MET cc_start: 0.8328 (mmm) cc_final: 0.8082 (tpp) REVERT: L 253 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8807 (t) REVERT: I 59 ASN cc_start: 0.8247 (m110) cc_final: 0.7877 (p0) REVERT: I 129 CYS cc_start: 0.7298 (m) cc_final: 0.6913 (m) REVERT: A 154 MET cc_start: 0.8565 (mmm) cc_final: 0.8321 (mmt) REVERT: A 439 SER cc_start: 0.7930 (m) cc_final: 0.7422 (p) REVERT: M 20 MET cc_start: 0.7266 (ttp) cc_final: 0.6472 (mtt) REVERT: M 28 LEU cc_start: 0.8098 (mp) cc_final: 0.7695 (mp) REVERT: M 32 TYR cc_start: 0.6879 (m-10) cc_final: 0.6625 (m-80) REVERT: M 37 GLN cc_start: 0.7197 (mt0) cc_final: 0.6789 (mt0) REVERT: M 100 LYS cc_start: 0.5788 (mmtp) cc_final: 0.5070 (ptmt) REVERT: K 253 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8591 (t) REVERT: K 431 ASP cc_start: 0.7602 (m-30) cc_final: 0.7321 (m-30) REVERT: H 59 ASN cc_start: 0.8459 (m110) cc_final: 0.8145 (p0) REVERT: H 75 MET cc_start: 0.8779 (mmt) cc_final: 0.8457 (mmt) REVERT: H 161 TYR cc_start: 0.8599 (m-80) cc_final: 0.8322 (m-80) REVERT: H 373 MET cc_start: 0.7990 (ptp) cc_final: 0.7779 (ptm) outliers start: 56 outliers final: 21 residues processed: 1016 average time/residue: 0.2356 time to fit residues: 382.8295 Evaluate side-chains 554 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 530 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 0.7980 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 HIS E 88 HIS E 186 ASN E 256 GLN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS F 101 ASN F 133 GLN ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 ASN F 406 HIS N 104 ASN J 88 HIS J 186 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN G 133 GLN G 228 ASN G 229 HIS G 309 HIS G 349 ASN C 28 HIS C 186 ASN C 283 HIS D 14 ASN D 133 GLN D 139 HIS D 228 ASN D 281 GLN L 18 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 283 HIS I 133 GLN I 139 HIS I 228 ASN I 229 HIS I 309 HIS A 28 HIS A 186 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 139 HIS B 228 ASN B 281 GLN M 104 ASN K 18 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN H 228 ASN H 229 HIS H 309 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.092744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077373 restraints weight = 87786.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080072 restraints weight = 39480.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081913 restraints weight = 23363.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083158 restraints weight = 16127.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.084006 restraints weight = 12435.975| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43998 Z= 0.154 Angle : 0.595 7.557 59746 Z= 0.321 Chirality : 0.043 0.160 6522 Planarity : 0.005 0.052 7776 Dihedral : 11.518 174.942 6168 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.84 % Allowed : 11.07 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.11), residues: 5388 helix: 2.37 (0.10), residues: 2438 sheet: 0.67 (0.18), residues: 768 loop : -0.65 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 123 TYR 0.018 0.001 TYR F 202 PHE 0.023 0.002 PHE L 267 TRP 0.012 0.002 TRP I 346 HIS 0.010 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00311 (43998) covalent geometry : angle 0.59533 (59746) hydrogen bonds : bond 0.05782 ( 2206) hydrogen bonds : angle 5.05247 ( 6408) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 607 time to evaluate : 1.473 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: E 77 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7782 (mm-30) REVERT: E 120 ASP cc_start: 0.8242 (m-30) cc_final: 0.7954 (m-30) REVERT: E 154 MET cc_start: 0.9263 (mmm) cc_final: 0.8249 (mmt) REVERT: E 205 ASP cc_start: 0.8062 (t0) cc_final: 0.7822 (t0) REVERT: E 211 ASP cc_start: 0.8169 (t0) cc_final: 0.7902 (t0) REVERT: E 297 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7846 (tm-30) REVERT: E 302 MET cc_start: 0.7863 (mtt) cc_final: 0.7384 (mtt) REVERT: F 269 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7860 (mtm) REVERT: F 314 THR cc_start: 0.8600 (p) cc_final: 0.8400 (p) REVERT: F 373 MET cc_start: 0.8289 (ptp) cc_final: 0.8082 (ptp) REVERT: N 32 TYR cc_start: 0.6668 (m-10) cc_final: 0.6159 (m-80) REVERT: J 297 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7587 (tm-30) REVERT: J 302 MET cc_start: 0.7218 (mtt) cc_final: 0.6929 (mtt) REVERT: J 352 LYS cc_start: 0.8209 (tttm) cc_final: 0.7748 (tppt) REVERT: G 47 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7393 (mm-30) REVERT: G 59 ASN cc_start: 0.8671 (m110) cc_final: 0.7940 (p0) REVERT: G 183 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: G 269 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8187 (mtm) REVERT: G 323 MET cc_start: 0.8867 (ptp) cc_final: 0.8497 (ptp) REVERT: G 349 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7988 (t0) REVERT: C 120 ASP cc_start: 0.8220 (m-30) cc_final: 0.7986 (m-30) REVERT: C 172 TYR cc_start: 0.8885 (t80) cc_final: 0.8581 (t80) REVERT: C 205 ASP cc_start: 0.8063 (t0) cc_final: 0.7820 (t0) REVERT: C 253 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8688 (m) REVERT: C 285 GLN cc_start: 0.8121 (pt0) cc_final: 0.7481 (mm110) REVERT: C 297 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8026 (tm-30) REVERT: D 202 TYR cc_start: 0.8634 (m-80) cc_final: 0.8406 (m-80) REVERT: D 299 LYS cc_start: 0.8390 (ptmt) cc_final: 0.7993 (tttp) REVERT: L 24 TYR cc_start: 0.8907 (m-80) cc_final: 0.8617 (m-80) REVERT: L 90 GLU cc_start: 0.8018 (mp0) cc_final: 0.7768 (mp0) REVERT: L 256 GLN cc_start: 0.8587 (pt0) cc_final: 0.7567 (tm-30) REVERT: L 284 GLU cc_start: 0.8132 (pt0) cc_final: 0.7653 (pm20) REVERT: I 59 ASN cc_start: 0.8537 (m110) cc_final: 0.7930 (p0) REVERT: I 161 TYR cc_start: 0.8459 (m-80) cc_final: 0.8226 (m-80) REVERT: I 200 GLU cc_start: 0.7865 (pt0) cc_final: 0.7630 (pt0) REVERT: I 205 ASP cc_start: 0.8312 (t0) cc_final: 0.8097 (t0) REVERT: I 299 LYS cc_start: 0.8407 (ptmt) cc_final: 0.8117 (tttp) REVERT: I 301 MET cc_start: 0.8457 (mmp) cc_final: 0.8227 (mmp) REVERT: A 154 MET cc_start: 0.9045 (mmm) cc_final: 0.7881 (mmt) REVERT: A 172 TYR cc_start: 0.8817 (t80) cc_final: 0.8595 (t80) REVERT: A 183 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 41 ASP cc_start: 0.6865 (p0) cc_final: 0.6645 (p0) REVERT: B 202 TYR cc_start: 0.8791 (m-80) cc_final: 0.8425 (m-10) REVERT: M 20 MET cc_start: 0.6988 (ttp) cc_final: 0.6443 (mtt) REVERT: M 32 TYR cc_start: 0.7011 (m-10) cc_final: 0.6541 (m-80) REVERT: M 100 LYS cc_start: 0.5589 (mmtp) cc_final: 0.4831 (ptmt) REVERT: K 123 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.8089 (tpp80) REVERT: K 186 ASN cc_start: 0.8930 (m-40) cc_final: 0.8693 (m110) REVERT: K 253 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8599 (m) REVERT: K 313 MET cc_start: 0.8329 (mtm) cc_final: 0.7920 (mpp) REVERT: K 413 MET cc_start: 0.7626 (ttm) cc_final: 0.7339 (ttm) REVERT: K 425 MET cc_start: 0.8273 (tpp) cc_final: 0.7816 (tpp) REVERT: K 431 ASP cc_start: 0.7503 (m-30) cc_final: 0.7213 (m-30) REVERT: H 47 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7607 (mm-30) REVERT: H 59 ASN cc_start: 0.8559 (m110) cc_final: 0.8084 (p0) REVERT: H 205 ASP cc_start: 0.8119 (t0) cc_final: 0.7832 (t0) REVERT: H 240 THR cc_start: 0.9278 (t) cc_final: 0.8962 (m) REVERT: H 332 MET cc_start: 0.9259 (mmm) cc_final: 0.8996 (mmm) REVERT: H 349 ASN cc_start: 0.7869 (m-40) cc_final: 0.7304 (t0) outliers start: 85 outliers final: 40 residues processed: 672 average time/residue: 0.2122 time to fit residues: 237.4206 Evaluate side-chains 517 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 471 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 349 ASN Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 213 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 93 optimal weight: 5.9990 chunk 525 optimal weight: 7.9990 chunk 374 optimal weight: 0.9990 chunk 440 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 338 optimal weight: 1.9990 chunk 512 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 HIS E 88 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS F 258 ASN F 293 GLN N 104 ASN J 8 HIS J 28 HIS J 88 HIS J 216 ASN J 283 HIS G 101 ASN G 139 HIS C 8 HIS D 258 ASN D 406 HIS L 8 HIS L 28 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 HIS A 88 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN B 258 ASN B 309 HIS B 406 HIS M 104 ASN K 8 HIS K 28 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072714 restraints weight = 90239.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075306 restraints weight = 42397.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077057 restraints weight = 25464.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078267 restraints weight = 18146.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079081 restraints weight = 14305.576| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 43998 Z= 0.214 Angle : 0.584 12.621 59746 Z= 0.309 Chirality : 0.044 0.155 6522 Planarity : 0.005 0.054 7776 Dihedral : 11.293 179.094 6155 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.82 % Allowed : 12.65 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.11), residues: 5388 helix: 2.31 (0.10), residues: 2460 sheet: 0.55 (0.18), residues: 756 loop : -0.62 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 2 TYR 0.027 0.002 TYR K 24 PHE 0.020 0.002 PHE N 107 TRP 0.013 0.002 TRP K 346 HIS 0.008 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00485 (43998) covalent geometry : angle 0.58428 (59746) hydrogen bonds : bond 0.05493 ( 2206) hydrogen bonds : angle 4.84588 ( 6408) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 471 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7888 (mm-30) REVERT: E 120 ASP cc_start: 0.8199 (m-30) cc_final: 0.7936 (m-30) REVERT: E 154 MET cc_start: 0.9051 (mmm) cc_final: 0.8737 (mmp) REVERT: E 205 ASP cc_start: 0.8225 (t0) cc_final: 0.7965 (t0) REVERT: E 211 ASP cc_start: 0.8288 (t0) cc_final: 0.7938 (t0) REVERT: E 302 MET cc_start: 0.7879 (mtt) cc_final: 0.7322 (mtt) REVERT: F 314 THR cc_start: 0.8683 (p) cc_final: 0.8432 (p) REVERT: F 332 MET cc_start: 0.8849 (mmp) cc_final: 0.8635 (mmp) REVERT: N 32 TYR cc_start: 0.6787 (m-10) cc_final: 0.6547 (m-80) REVERT: N 35 ILE cc_start: 0.7953 (mp) cc_final: 0.7503 (mt) REVERT: N 96 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.6032 (mp) REVERT: N 100 LYS cc_start: 0.4826 (mmtp) cc_final: 0.4056 (ptmt) REVERT: N 118 ASN cc_start: 0.3766 (m-40) cc_final: 0.3523 (m110) REVERT: J 297 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7388 (tm-30) REVERT: J 302 MET cc_start: 0.7785 (mtt) cc_final: 0.7457 (mtt) REVERT: G 47 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7547 (mm-30) REVERT: G 75 MET cc_start: 0.9158 (mmt) cc_final: 0.8476 (mmt) REVERT: G 269 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: G 323 MET cc_start: 0.8804 (ptp) cc_final: 0.7983 (ptp) REVERT: C 120 ASP cc_start: 0.8171 (m-30) cc_final: 0.7914 (m-30) REVERT: C 123 ARG cc_start: 0.8554 (tpp80) cc_final: 0.8336 (tpp80) REVERT: C 205 ASP cc_start: 0.8229 (t0) cc_final: 0.7952 (t0) REVERT: C 285 GLN cc_start: 0.8193 (pt0) cc_final: 0.7564 (mm110) REVERT: C 338 LYS cc_start: 0.8240 (tptt) cc_final: 0.7934 (tptp) REVERT: C 425 MET cc_start: 0.8677 (tpp) cc_final: 0.8397 (tpp) REVERT: D 254 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8609 (ttmt) REVERT: D 299 LYS cc_start: 0.8610 (ptmt) cc_final: 0.8225 (tttp) REVERT: L 24 TYR cc_start: 0.8974 (m-80) cc_final: 0.8730 (m-80) REVERT: L 127 ASP cc_start: 0.8209 (m-30) cc_final: 0.7864 (m-30) REVERT: L 284 GLU cc_start: 0.8207 (pt0) cc_final: 0.7714 (pm20) REVERT: L 313 MET cc_start: 0.8191 (mtm) cc_final: 0.7987 (mtm) REVERT: I 145 THR cc_start: 0.8778 (m) cc_final: 0.8407 (p) REVERT: I 149 MET cc_start: 0.8824 (ttt) cc_final: 0.8543 (ttt) REVERT: I 200 GLU cc_start: 0.8017 (pt0) cc_final: 0.7632 (pt0) REVERT: I 299 LYS cc_start: 0.8565 (ptmt) cc_final: 0.8353 (tttp) REVERT: I 301 MET cc_start: 0.8591 (mmp) cc_final: 0.8297 (mmp) REVERT: A 154 MET cc_start: 0.8802 (mmm) cc_final: 0.8402 (mmm) REVERT: A 168 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 183 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 211 ASP cc_start: 0.8240 (t0) cc_final: 0.8017 (t0) REVERT: A 382 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8719 (p) REVERT: M 32 TYR cc_start: 0.6963 (m-10) cc_final: 0.6350 (m-80) REVERT: M 95 LYS cc_start: 0.7293 (mttm) cc_final: 0.6673 (mmtt) REVERT: M 100 LYS cc_start: 0.5433 (mmtp) cc_final: 0.4826 (ptmt) REVERT: K 313 MET cc_start: 0.8455 (mtm) cc_final: 0.8231 (mtm) REVERT: H 26 ASP cc_start: 0.8326 (t0) cc_final: 0.7923 (t0) REVERT: H 47 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7515 (mm-30) REVERT: H 254 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8485 (ttpt) REVERT: H 269 MET cc_start: 0.8456 (ptm) cc_final: 0.8143 (ptp) REVERT: H 349 ASN cc_start: 0.8144 (m-40) cc_final: 0.7590 (t0) outliers start: 130 outliers final: 68 residues processed: 566 average time/residue: 0.2146 time to fit residues: 203.3736 Evaluate side-chains 501 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 427 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 163 LYS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 256 optimal weight: 2.9990 chunk 458 optimal weight: 5.9990 chunk 420 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 493 optimal weight: 7.9990 chunk 328 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 222 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 HIS G 331 GLN G 433 GLN D 229 HIS D 331 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 GLN I 436 GLN A 18 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS H 331 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073601 restraints weight = 89902.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076275 restraints weight = 42040.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078114 restraints weight = 25486.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079333 restraints weight = 18069.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.080162 restraints weight = 14263.427| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43998 Z= 0.133 Angle : 0.520 12.418 59746 Z= 0.272 Chirality : 0.042 0.162 6522 Planarity : 0.004 0.046 7776 Dihedral : 11.115 178.865 6152 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.34 % Allowed : 13.56 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.11), residues: 5388 helix: 2.28 (0.10), residues: 2498 sheet: 0.59 (0.18), residues: 768 loop : -0.65 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 221 TYR 0.021 0.001 TYR K 24 PHE 0.014 0.001 PHE M 114 TRP 0.012 0.001 TRP E 346 HIS 0.005 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00288 (43998) covalent geometry : angle 0.52038 (59746) hydrogen bonds : bond 0.04676 ( 2206) hydrogen bonds : angle 4.61389 ( 6408) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 490 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7848 (mm-30) REVERT: E 120 ASP cc_start: 0.8206 (m-30) cc_final: 0.7911 (m-30) REVERT: E 154 MET cc_start: 0.9248 (mmm) cc_final: 0.8770 (mmp) REVERT: E 205 ASP cc_start: 0.8121 (t0) cc_final: 0.7845 (t0) REVERT: E 211 ASP cc_start: 0.8239 (t0) cc_final: 0.7845 (t0) REVERT: F 138 THR cc_start: 0.9012 (m) cc_final: 0.8494 (p) REVERT: F 200 GLU cc_start: 0.8032 (pt0) cc_final: 0.7830 (pt0) REVERT: F 235 MET cc_start: 0.8254 (mtm) cc_final: 0.7812 (mtp) REVERT: F 269 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8052 (mtm) REVERT: F 332 MET cc_start: 0.8865 (mmp) cc_final: 0.8639 (mmp) REVERT: N 100 LYS cc_start: 0.4727 (mmtp) cc_final: 0.4022 (ptmt) REVERT: J 36 MET cc_start: 0.8396 (ptm) cc_final: 0.8165 (ptm) REVERT: J 172 TYR cc_start: 0.8801 (t80) cc_final: 0.8421 (t80) REVERT: J 297 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7385 (tm-30) REVERT: J 302 MET cc_start: 0.7883 (mtt) cc_final: 0.7515 (ttm) REVERT: G 47 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7554 (mm-30) REVERT: G 75 MET cc_start: 0.9128 (mmt) cc_final: 0.8504 (mmt) REVERT: G 269 MET cc_start: 0.8401 (mtp) cc_final: 0.8095 (mtm) REVERT: G 323 MET cc_start: 0.8747 (ptp) cc_final: 0.8134 (ptp) REVERT: C 120 ASP cc_start: 0.8127 (m-30) cc_final: 0.7767 (m-30) REVERT: C 205 ASP cc_start: 0.8226 (t0) cc_final: 0.7847 (t0) REVERT: C 338 LYS cc_start: 0.8343 (tptt) cc_final: 0.8106 (tptt) REVERT: C 425 MET cc_start: 0.8678 (tpp) cc_final: 0.8395 (tpp) REVERT: L 127 ASP cc_start: 0.8202 (m-30) cc_final: 0.7933 (m-30) REVERT: L 230 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8712 (mp) REVERT: L 284 GLU cc_start: 0.8152 (pt0) cc_final: 0.7685 (pm20) REVERT: L 313 MET cc_start: 0.8209 (mtm) cc_final: 0.7702 (mtm) REVERT: L 413 MET cc_start: 0.7801 (ttm) cc_final: 0.7524 (tpp) REVERT: I 59 ASN cc_start: 0.8513 (m-40) cc_final: 0.7960 (p0) REVERT: I 123 ARG cc_start: 0.8832 (ttm110) cc_final: 0.8249 (mtm180) REVERT: I 145 THR cc_start: 0.8607 (m) cc_final: 0.8358 (p) REVERT: I 200 GLU cc_start: 0.7926 (pt0) cc_final: 0.7552 (pt0) REVERT: I 301 MET cc_start: 0.8552 (mmp) cc_final: 0.8257 (mmp) REVERT: A 120 ASP cc_start: 0.8025 (m-30) cc_final: 0.7824 (m-30) REVERT: A 127 ASP cc_start: 0.8696 (m-30) cc_final: 0.8287 (m-30) REVERT: A 183 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 211 ASP cc_start: 0.8234 (t0) cc_final: 0.7958 (t0) REVERT: A 253 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8677 (m) REVERT: A 297 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 309 HIS cc_start: 0.7563 (m90) cc_final: 0.7002 (m90) REVERT: A 338 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7515 (mttt) REVERT: A 382 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8705 (p) REVERT: B 41 ASP cc_start: 0.7335 (p0) cc_final: 0.7125 (p0) REVERT: B 47 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 202 TYR cc_start: 0.8781 (m-80) cc_final: 0.8227 (m-10) REVERT: B 205 ASP cc_start: 0.8037 (m-30) cc_final: 0.7826 (t0) REVERT: B 299 LYS cc_start: 0.8624 (ptmt) cc_final: 0.8325 (ttpt) REVERT: M 32 TYR cc_start: 0.6879 (m-10) cc_final: 0.6479 (m-80) REVERT: M 34 LYS cc_start: 0.7379 (mmmt) cc_final: 0.6875 (mppt) REVERT: M 37 GLN cc_start: 0.7015 (mp10) cc_final: 0.6574 (mp10) REVERT: M 48 MET cc_start: 0.6118 (ttp) cc_final: 0.5661 (tmm) REVERT: M 95 LYS cc_start: 0.7255 (mttm) cc_final: 0.6634 (mmtt) REVERT: M 96 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5835 (mp) REVERT: M 100 LYS cc_start: 0.5006 (mmtp) cc_final: 0.4399 (ptmt) REVERT: K 425 MET cc_start: 0.8511 (tpp) cc_final: 0.8292 (tpp) REVERT: K 431 ASP cc_start: 0.7528 (m-30) cc_final: 0.7310 (m-30) REVERT: H 26 ASP cc_start: 0.8370 (t0) cc_final: 0.8006 (t0) REVERT: H 47 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7541 (mm-30) REVERT: H 205 ASP cc_start: 0.8222 (t0) cc_final: 0.7986 (t0) REVERT: H 240 THR cc_start: 0.9311 (t) cc_final: 0.8881 (m) REVERT: H 254 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8443 (ttpt) REVERT: H 349 ASN cc_start: 0.8238 (m-40) cc_final: 0.7732 (t0) REVERT: H 435 TYR cc_start: 0.8785 (m-80) cc_final: 0.8402 (m-10) outliers start: 108 outliers final: 58 residues processed: 573 average time/residue: 0.2120 time to fit residues: 202.7379 Evaluate side-chains 493 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 429 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 323 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 266 optimal weight: 8.9990 chunk 296 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 357 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 531 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 339 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS E 216 ASN E 283 HIS F 293 GLN F 433 GLN N 118 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS H 107 HIS H 433 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071917 restraints weight = 90870.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074537 restraints weight = 42719.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076329 restraints weight = 26090.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077514 restraints weight = 18649.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078332 restraints weight = 14794.986| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43998 Z= 0.187 Angle : 0.546 11.869 59746 Z= 0.284 Chirality : 0.043 0.150 6522 Planarity : 0.004 0.048 7776 Dihedral : 11.106 177.175 6150 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.47 % Allowed : 13.82 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.11), residues: 5388 helix: 2.23 (0.10), residues: 2506 sheet: 0.46 (0.18), residues: 768 loop : -0.70 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 215 TYR 0.029 0.001 TYR K 24 PHE 0.019 0.001 PHE N 107 TRP 0.012 0.002 TRP K 346 HIS 0.005 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00424 (43998) covalent geometry : angle 0.54576 (59746) hydrogen bonds : bond 0.04888 ( 2206) hydrogen bonds : angle 4.64817 ( 6408) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 454 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8134 (m-30) cc_final: 0.7831 (m-30) REVERT: E 154 MET cc_start: 0.9189 (mmm) cc_final: 0.8703 (mmp) REVERT: E 205 ASP cc_start: 0.8241 (t0) cc_final: 0.7952 (t0) REVERT: E 211 ASP cc_start: 0.8282 (t0) cc_final: 0.7875 (t0) REVERT: E 297 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8097 (tm-30) REVERT: E 309 HIS cc_start: 0.7491 (m90) cc_final: 0.6775 (m90) REVERT: F 138 THR cc_start: 0.8930 (m) cc_final: 0.8598 (p) REVERT: F 235 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7717 (mtp) REVERT: F 332 MET cc_start: 0.8858 (mmp) cc_final: 0.8649 (mmp) REVERT: N 85 MET cc_start: 0.7045 (mmt) cc_final: 0.6624 (mmm) REVERT: N 95 LYS cc_start: 0.7624 (mttm) cc_final: 0.6790 (mtmt) REVERT: N 100 LYS cc_start: 0.4835 (mmtp) cc_final: 0.4128 (ptmt) REVERT: J 172 TYR cc_start: 0.8821 (t80) cc_final: 0.8517 (t80) REVERT: J 297 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7373 (tm-30) REVERT: J 302 MET cc_start: 0.7943 (mtt) cc_final: 0.7658 (ttm) REVERT: J 352 LYS cc_start: 0.8359 (tttm) cc_final: 0.7917 (tppt) REVERT: G 47 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7524 (mm-30) REVERT: G 75 MET cc_start: 0.9153 (mmt) cc_final: 0.8513 (mmt) REVERT: G 138 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8398 (p) REVERT: G 269 MET cc_start: 0.8406 (mtp) cc_final: 0.8181 (mtm) REVERT: G 323 MET cc_start: 0.8742 (ptp) cc_final: 0.8085 (ptp) REVERT: G 393 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7949 (mm-30) REVERT: C 120 ASP cc_start: 0.8142 (m-30) cc_final: 0.7787 (m-30) REVERT: C 205 ASP cc_start: 0.8297 (t0) cc_final: 0.7914 (t0) REVERT: C 297 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7959 (tm-30) REVERT: C 425 MET cc_start: 0.8838 (tpp) cc_final: 0.8592 (tpp) REVERT: L 127 ASP cc_start: 0.8211 (m-30) cc_final: 0.7949 (m-30) REVERT: L 230 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8732 (mp) REVERT: L 284 GLU cc_start: 0.8158 (pt0) cc_final: 0.7698 (pm20) REVERT: L 313 MET cc_start: 0.8197 (mtm) cc_final: 0.7742 (mtm) REVERT: L 431 ASP cc_start: 0.7850 (m-30) cc_final: 0.7594 (m-30) REVERT: I 59 ASN cc_start: 0.8592 (m-40) cc_final: 0.8017 (p0) REVERT: I 123 ARG cc_start: 0.8799 (ttm110) cc_final: 0.8187 (mtm180) REVERT: I 145 THR cc_start: 0.8613 (m) cc_final: 0.8387 (p) REVERT: I 200 GLU cc_start: 0.7907 (pt0) cc_final: 0.7547 (pt0) REVERT: A 120 ASP cc_start: 0.8057 (m-30) cc_final: 0.7841 (m-30) REVERT: A 127 ASP cc_start: 0.8714 (m-30) cc_final: 0.8302 (m-30) REVERT: A 211 ASP cc_start: 0.8270 (t0) cc_final: 0.7978 (t0) REVERT: A 382 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8802 (p) REVERT: B 278 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8244 (mmm160) REVERT: B 308 ARG cc_start: 0.8373 (mtt90) cc_final: 0.8154 (ptp90) REVERT: M 32 TYR cc_start: 0.6931 (m-10) cc_final: 0.6420 (m-80) REVERT: M 34 LYS cc_start: 0.7389 (mmmt) cc_final: 0.6945 (mppt) REVERT: M 37 GLN cc_start: 0.7075 (mp10) cc_final: 0.6703 (mp10) REVERT: M 48 MET cc_start: 0.6101 (ttp) cc_final: 0.5792 (tmm) REVERT: M 95 LYS cc_start: 0.7403 (mttm) cc_final: 0.6883 (mmtt) REVERT: M 100 LYS cc_start: 0.5166 (mmtp) cc_final: 0.4543 (ptmt) REVERT: K 18 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8045 (m110) REVERT: K 172 TYR cc_start: 0.8943 (t80) cc_final: 0.8538 (t80) REVERT: K 425 MET cc_start: 0.8662 (tpp) cc_final: 0.8421 (tpp) REVERT: H 26 ASP cc_start: 0.8347 (t0) cc_final: 0.7983 (t0) REVERT: H 47 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7499 (mm-30) REVERT: H 205 ASP cc_start: 0.8178 (t0) cc_final: 0.7904 (t0) REVERT: H 254 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8435 (ttpt) REVERT: H 349 ASN cc_start: 0.8267 (m-40) cc_final: 0.7776 (t0) REVERT: H 435 TYR cc_start: 0.8814 (m-80) cc_final: 0.8452 (m-10) outliers start: 114 outliers final: 79 residues processed: 538 average time/residue: 0.2683 time to fit residues: 240.8864 Evaluate side-chains 505 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 420 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 323 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 220 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 249 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 292 optimal weight: 0.8980 chunk 464 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 392 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS F 247 GLN G 258 ASN D 247 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 HIS I 258 ASN I 433 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070221 restraints weight = 92170.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.072752 restraints weight = 43505.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.074522 restraints weight = 26696.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075656 restraints weight = 19062.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076458 restraints weight = 15163.969| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 43998 Z= 0.253 Angle : 0.594 9.159 59746 Z= 0.310 Chirality : 0.044 0.179 6522 Planarity : 0.004 0.050 7776 Dihedral : 11.250 179.763 6148 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.82 % Allowed : 14.72 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.11), residues: 5388 helix: 2.12 (0.10), residues: 2496 sheet: 0.32 (0.18), residues: 750 loop : -0.72 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 278 TYR 0.032 0.002 TYR L 24 PHE 0.020 0.002 PHE N 107 TRP 0.012 0.002 TRP E 21 HIS 0.006 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00577 (43998) covalent geometry : angle 0.59427 (59746) hydrogen bonds : bond 0.05280 ( 2206) hydrogen bonds : angle 4.75865 ( 6408) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 434 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8156 (m-30) cc_final: 0.7844 (m-30) REVERT: E 205 ASP cc_start: 0.8337 (t0) cc_final: 0.8026 (t0) REVERT: E 211 ASP cc_start: 0.8323 (t0) cc_final: 0.7907 (t0) REVERT: E 297 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8075 (tm-30) REVERT: F 235 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7835 (mtp) REVERT: F 332 MET cc_start: 0.8867 (mmp) cc_final: 0.8630 (mmp) REVERT: N 35 ILE cc_start: 0.7998 (mp) cc_final: 0.7631 (mt) REVERT: N 85 MET cc_start: 0.7100 (mmt) cc_final: 0.6540 (mpp) REVERT: N 95 LYS cc_start: 0.7692 (mttm) cc_final: 0.7022 (mmpt) REVERT: N 100 LYS cc_start: 0.4821 (mmtp) cc_final: 0.4211 (ptmt) REVERT: J 127 ASP cc_start: 0.8240 (m-30) cc_final: 0.7754 (m-30) REVERT: J 172 TYR cc_start: 0.8855 (t80) cc_final: 0.8602 (t80) REVERT: J 297 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7545 (tm-30) REVERT: J 352 LYS cc_start: 0.8416 (tttm) cc_final: 0.8028 (tppt) REVERT: J 413 MET cc_start: 0.8163 (ttm) cc_final: 0.7958 (ttm) REVERT: G 47 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7537 (mm-30) REVERT: G 75 MET cc_start: 0.9187 (mmt) cc_final: 0.8572 (mmt) REVERT: G 138 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8443 (p) REVERT: G 269 MET cc_start: 0.8260 (mtp) cc_final: 0.7947 (mtp) REVERT: G 323 MET cc_start: 0.8721 (ptp) cc_final: 0.8073 (ptp) REVERT: G 393 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7812 (mm-30) REVERT: C 120 ASP cc_start: 0.8143 (m-30) cc_final: 0.7888 (m-30) REVERT: C 168 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7238 (mt-10) REVERT: C 205 ASP cc_start: 0.8350 (t0) cc_final: 0.8010 (t0) REVERT: C 425 MET cc_start: 0.8792 (tpp) cc_final: 0.8591 (tpp) REVERT: D 37 HIS cc_start: 0.7773 (m90) cc_final: 0.7469 (m90) REVERT: D 373 MET cc_start: 0.8254 (ttp) cc_final: 0.7949 (ttp) REVERT: L 127 ASP cc_start: 0.8184 (m-30) cc_final: 0.7889 (m-30) REVERT: L 431 ASP cc_start: 0.7861 (m-30) cc_final: 0.7604 (m-30) REVERT: I 123 ARG cc_start: 0.8784 (ttm110) cc_final: 0.8154 (mtm180) REVERT: I 200 GLU cc_start: 0.7958 (pt0) cc_final: 0.7726 (pt0) REVERT: A 120 ASP cc_start: 0.8093 (m-30) cc_final: 0.7863 (m-30) REVERT: A 183 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 211 ASP cc_start: 0.8259 (t0) cc_final: 0.7957 (t0) REVERT: B 299 LYS cc_start: 0.8720 (ptmt) cc_final: 0.8357 (tmtt) REVERT: B 373 MET cc_start: 0.7971 (ptp) cc_final: 0.7731 (ptp) REVERT: M 32 TYR cc_start: 0.6981 (m-10) cc_final: 0.6665 (m-80) REVERT: M 34 LYS cc_start: 0.7323 (mmmt) cc_final: 0.6880 (mppt) REVERT: M 37 GLN cc_start: 0.7026 (mp10) cc_final: 0.6635 (mp10) REVERT: M 48 MET cc_start: 0.6054 (ttp) cc_final: 0.5752 (tmm) REVERT: M 95 LYS cc_start: 0.7424 (mttm) cc_final: 0.6899 (mmtt) REVERT: M 96 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5827 (mp) REVERT: M 100 LYS cc_start: 0.5090 (mmtp) cc_final: 0.4537 (ptmt) REVERT: K 18 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8184 (m110) REVERT: K 425 MET cc_start: 0.8708 (tpp) cc_final: 0.8434 (tpp) REVERT: H 26 ASP cc_start: 0.8387 (t0) cc_final: 0.8014 (t0) REVERT: H 205 ASP cc_start: 0.8104 (t0) cc_final: 0.7898 (t0) REVERT: H 349 ASN cc_start: 0.8326 (m-40) cc_final: 0.7743 (t0) outliers start: 130 outliers final: 96 residues processed: 530 average time/residue: 0.2612 time to fit residues: 231.2524 Evaluate side-chains 509 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 409 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 436 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 35 optimal weight: 0.0570 chunk 446 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 245 optimal weight: 1.9990 chunk 463 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 397 optimal weight: 4.9990 chunk 481 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS N 118 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS A 18 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** 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 = 0.3506 r_free = 0.3506 target = 0.087537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071399 restraints weight = 90787.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073980 restraints weight = 42954.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075774 restraints weight = 26270.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076924 restraints weight = 18714.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077744 restraints weight = 14912.833| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 43998 Z= 0.166 Angle : 0.546 10.141 59746 Z= 0.283 Chirality : 0.042 0.142 6522 Planarity : 0.004 0.048 7776 Dihedral : 11.175 179.556 6145 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.88 % Allowed : 15.31 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.11), residues: 5388 helix: 2.17 (0.10), residues: 2504 sheet: 0.30 (0.18), residues: 756 loop : -0.67 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 278 TYR 0.022 0.001 TYR L 24 PHE 0.015 0.001 PHE N 107 TRP 0.014 0.001 TRP E 21 HIS 0.005 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00374 (43998) covalent geometry : angle 0.54595 (59746) hydrogen bonds : bond 0.04766 ( 2206) hydrogen bonds : angle 4.61672 ( 6408) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 442 time to evaluate : 1.435 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: E 120 ASP cc_start: 0.8138 (m-30) cc_final: 0.7815 (m-30) REVERT: E 205 ASP cc_start: 0.8266 (t0) cc_final: 0.7933 (t0) REVERT: E 211 ASP cc_start: 0.8319 (t0) cc_final: 0.7897 (t0) REVERT: E 297 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8107 (tm-30) REVERT: E 338 LYS cc_start: 0.7934 (tptt) cc_final: 0.7475 (ttpt) REVERT: F 41 ASP cc_start: 0.7519 (p0) cc_final: 0.7225 (p0) REVERT: F 47 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7851 (mm-30) REVERT: F 138 THR cc_start: 0.9025 (m) cc_final: 0.8685 (p) REVERT: F 235 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7621 (mtp) REVERT: F 299 LYS cc_start: 0.8709 (tttp) cc_final: 0.8477 (tmtt) REVERT: F 332 MET cc_start: 0.8882 (mmp) cc_final: 0.8640 (mmp) REVERT: N 35 ILE cc_start: 0.7983 (mp) cc_final: 0.7610 (mt) REVERT: N 95 LYS cc_start: 0.7699 (mttm) cc_final: 0.7017 (mmpt) REVERT: N 100 LYS cc_start: 0.4973 (mmtp) cc_final: 0.4200 (ptmt) REVERT: J 172 TYR cc_start: 0.8814 (t80) cc_final: 0.8571 (t80) REVERT: J 297 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7335 (tm-30) REVERT: J 352 LYS cc_start: 0.8442 (tttm) cc_final: 0.8099 (tppt) REVERT: J 377 MET cc_start: 0.8397 (ttp) cc_final: 0.8187 (ttp) REVERT: J 413 MET cc_start: 0.8037 (ttm) cc_final: 0.7814 (ttm) REVERT: G 47 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7706 (mm-30) REVERT: G 75 MET cc_start: 0.9177 (mmt) cc_final: 0.8631 (mmt) REVERT: G 138 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8405 (p) REVERT: G 323 MET cc_start: 0.8664 (ptp) cc_final: 0.8281 (ptp) REVERT: G 332 MET cc_start: 0.9159 (mmt) cc_final: 0.8952 (mmm) REVERT: G 393 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7882 (mm-30) REVERT: C 120 ASP cc_start: 0.8138 (m-30) cc_final: 0.7788 (m-30) REVERT: C 205 ASP cc_start: 0.8350 (t0) cc_final: 0.8012 (t0) REVERT: C 425 MET cc_start: 0.8875 (tpp) cc_final: 0.8656 (tpp) REVERT: D 37 HIS cc_start: 0.7734 (m90) cc_final: 0.7479 (m90) REVERT: D 69 ASP cc_start: 0.7921 (t0) cc_final: 0.7636 (t0) REVERT: D 373 MET cc_start: 0.8064 (ttp) cc_final: 0.7673 (ttp) REVERT: L 127 ASP cc_start: 0.8167 (m-30) cc_final: 0.7715 (m-30) REVERT: L 431 ASP cc_start: 0.7859 (m-30) cc_final: 0.7624 (m-30) REVERT: I 59 ASN cc_start: 0.8586 (m-40) cc_final: 0.8108 (p0) REVERT: I 123 ARG cc_start: 0.8800 (ttm110) cc_final: 0.8172 (mtm180) REVERT: I 200 GLU cc_start: 0.7867 (pt0) cc_final: 0.7648 (pt0) REVERT: I 315 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8805 (m) REVERT: A 120 ASP cc_start: 0.8120 (m-30) cc_final: 0.7892 (m-30) REVERT: A 183 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 211 ASP cc_start: 0.8250 (t0) cc_final: 0.7947 (t0) REVERT: A 382 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8888 (p) REVERT: B 259 MET cc_start: 0.8904 (mmm) cc_final: 0.8554 (mmp) REVERT: B 278 ARG cc_start: 0.8554 (mmm160) cc_final: 0.8320 (mmm160) REVERT: M 32 TYR cc_start: 0.6958 (m-10) cc_final: 0.6683 (m-80) REVERT: M 34 LYS cc_start: 0.7310 (mmmt) cc_final: 0.6834 (mppt) REVERT: M 35 ILE cc_start: 0.7801 (mp) cc_final: 0.7314 (mt) REVERT: M 37 GLN cc_start: 0.7069 (mp10) cc_final: 0.6753 (mp10) REVERT: M 48 MET cc_start: 0.5970 (ttp) cc_final: 0.5431 (tmm) REVERT: M 95 LYS cc_start: 0.7448 (mttm) cc_final: 0.6901 (mmtt) REVERT: M 96 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5768 (mp) REVERT: M 100 LYS cc_start: 0.5034 (mmtp) cc_final: 0.4510 (ptmt) REVERT: K 18 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8055 (m110) REVERT: H 26 ASP cc_start: 0.8367 (t0) cc_final: 0.8053 (t0) REVERT: H 205 ASP cc_start: 0.8091 (t0) cc_final: 0.7787 (t0) REVERT: H 212 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8852 (mp) REVERT: H 349 ASN cc_start: 0.8319 (m-40) cc_final: 0.7730 (t0) REVERT: H 435 TYR cc_start: 0.8738 (m-80) cc_final: 0.8439 (m-10) outliers start: 133 outliers final: 94 residues processed: 541 average time/residue: 0.2067 time to fit residues: 187.5269 Evaluate side-chains 519 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 418 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 323 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 408 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 412 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 438 optimal weight: 20.0000 chunk 291 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 358 optimal weight: 0.1980 chunk 306 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN E 88 HIS E 107 HIS N 118 ASN J 107 HIS C 18 ASN C 329 ASN D 107 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 433 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073487 restraints weight = 90760.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076125 restraints weight = 42406.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077921 restraints weight = 25706.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.079114 restraints weight = 18245.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079935 restraints weight = 14397.341| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43998 Z= 0.118 Angle : 0.530 10.847 59746 Z= 0.271 Chirality : 0.041 0.221 6522 Planarity : 0.004 0.046 7776 Dihedral : 11.046 179.478 6144 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.38 % Allowed : 16.02 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.11), residues: 5388 helix: 2.24 (0.10), residues: 2510 sheet: 0.30 (0.18), residues: 768 loop : -0.58 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 278 TYR 0.021 0.001 TYR K 24 PHE 0.013 0.001 PHE I 377 TRP 0.016 0.001 TRP E 21 HIS 0.006 0.001 HIS J 309 Details of bonding type rmsd covalent geometry : bond 0.00257 (43998) covalent geometry : angle 0.52962 (59746) hydrogen bonds : bond 0.04241 ( 2206) hydrogen bonds : angle 4.50405 ( 6408) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 474 time to evaluate : 1.557 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: E 120 ASP cc_start: 0.8159 (m-30) cc_final: 0.7837 (m-30) REVERT: E 168 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7017 (mt-10) REVERT: E 205 ASP cc_start: 0.8126 (t0) cc_final: 0.7858 (t0) REVERT: E 211 ASP cc_start: 0.8282 (t0) cc_final: 0.7872 (t0) REVERT: E 297 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8055 (tm-30) REVERT: F 41 ASP cc_start: 0.7511 (p0) cc_final: 0.7205 (p0) REVERT: F 47 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7701 (mm-30) REVERT: F 137 LEU cc_start: 0.8804 (tt) cc_final: 0.8484 (tp) REVERT: F 138 THR cc_start: 0.8936 (m) cc_final: 0.8606 (p) REVERT: F 235 MET cc_start: 0.8078 (mtm) cc_final: 0.7691 (mtp) REVERT: F 299 LYS cc_start: 0.8763 (tttp) cc_final: 0.8531 (tmtt) REVERT: F 332 MET cc_start: 0.8919 (mmp) cc_final: 0.8692 (mmp) REVERT: N 35 ILE cc_start: 0.7932 (mp) cc_final: 0.7553 (mt) REVERT: N 95 LYS cc_start: 0.7699 (mttm) cc_final: 0.7023 (mmpt) REVERT: N 100 LYS cc_start: 0.4893 (mmtp) cc_final: 0.4193 (ptmt) REVERT: J 172 TYR cc_start: 0.8781 (t80) cc_final: 0.8531 (t80) REVERT: J 297 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7351 (tm-30) REVERT: J 352 LYS cc_start: 0.8405 (tttm) cc_final: 0.7995 (tppt) REVERT: J 413 MET cc_start: 0.7981 (ttm) cc_final: 0.7710 (ttm) REVERT: J 425 MET cc_start: 0.8693 (tpp) cc_final: 0.8194 (tpp) REVERT: J 431 ASP cc_start: 0.7559 (m-30) cc_final: 0.7259 (m-30) REVERT: G 47 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7559 (mm-30) REVERT: G 75 MET cc_start: 0.9119 (mmt) cc_final: 0.8660 (mmt) REVERT: G 138 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8413 (p) REVERT: G 269 MET cc_start: 0.8403 (mtm) cc_final: 0.8031 (mtp) REVERT: G 323 MET cc_start: 0.8602 (ptp) cc_final: 0.8380 (ptp) REVERT: G 332 MET cc_start: 0.9125 (mmt) cc_final: 0.8884 (mmm) REVERT: G 393 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7841 (mm-30) REVERT: C 120 ASP cc_start: 0.8131 (m-30) cc_final: 0.7789 (m-30) REVERT: C 205 ASP cc_start: 0.8149 (t0) cc_final: 0.7760 (t0) REVERT: D 37 HIS cc_start: 0.7705 (m90) cc_final: 0.7478 (m90) REVERT: D 69 ASP cc_start: 0.7755 (t0) cc_final: 0.7545 (t0) REVERT: D 101 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8389 (t0) REVERT: D 373 MET cc_start: 0.8049 (ttp) cc_final: 0.7631 (ttp) REVERT: L 127 ASP cc_start: 0.8146 (m-30) cc_final: 0.7704 (m-30) REVERT: L 275 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8682 (p) REVERT: L 431 ASP cc_start: 0.7760 (m-30) cc_final: 0.7499 (m-30) REVERT: I 59 ASN cc_start: 0.8554 (m-40) cc_final: 0.8115 (p0) REVERT: I 123 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8172 (mtm180) REVERT: I 315 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8677 (m) REVERT: A 120 ASP cc_start: 0.8099 (m-30) cc_final: 0.7874 (m-30) REVERT: A 183 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 211 ASP cc_start: 0.8123 (t0) cc_final: 0.7806 (t0) REVERT: A 382 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8971 (p) REVERT: B 278 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8390 (mmm160) REVERT: M 32 TYR cc_start: 0.7015 (m-10) cc_final: 0.6728 (m-80) REVERT: M 37 GLN cc_start: 0.7275 (mp10) cc_final: 0.7033 (mp10) REVERT: M 48 MET cc_start: 0.6069 (ttp) cc_final: 0.5604 (tmm) REVERT: M 95 LYS cc_start: 0.7387 (mttm) cc_final: 0.6823 (mmtt) REVERT: M 96 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5836 (mp) REVERT: M 100 LYS cc_start: 0.5121 (mmtp) cc_final: 0.4627 (ptmt) REVERT: K 18 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.7916 (m110) REVERT: H 26 ASP cc_start: 0.8304 (t0) cc_final: 0.7964 (t0) REVERT: H 212 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8858 (mp) REVERT: H 349 ASN cc_start: 0.8338 (m-40) cc_final: 0.7736 (t0) REVERT: H 435 TYR cc_start: 0.8553 (m-80) cc_final: 0.8347 (m-10) outliers start: 110 outliers final: 80 residues processed: 554 average time/residue: 0.2192 time to fit residues: 203.9357 Evaluate side-chains 527 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 439 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 323 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 240 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 461 optimal weight: 0.7980 chunk 504 optimal weight: 2.9990 chunk 384 optimal weight: 0.9990 chunk 437 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 118 ASN G 107 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.088966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073713 restraints weight = 90163.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076331 restraints weight = 40964.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078050 restraints weight = 24203.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.079216 restraints weight = 16909.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080004 restraints weight = 13179.580| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43998 Z= 0.129 Angle : 0.541 10.672 59746 Z= 0.275 Chirality : 0.042 0.172 6522 Planarity : 0.004 0.046 7776 Dihedral : 11.008 179.135 6144 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.30 % Allowed : 16.57 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.11), residues: 5388 helix: 2.25 (0.10), residues: 2510 sheet: 0.33 (0.18), residues: 768 loop : -0.56 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 278 TYR 0.030 0.001 TYR K 24 PHE 0.020 0.001 PHE I 262 TRP 0.014 0.001 TRP E 346 HIS 0.003 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00292 (43998) covalent geometry : angle 0.54067 (59746) hydrogen bonds : bond 0.04251 ( 2206) hydrogen bonds : angle 4.50740 ( 6408) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 455 time to evaluate : 1.304 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: E 120 ASP cc_start: 0.8173 (m-30) cc_final: 0.7836 (m-30) REVERT: E 127 ASP cc_start: 0.8538 (m-30) cc_final: 0.8086 (m-30) REVERT: E 168 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6972 (mt-10) REVERT: E 205 ASP cc_start: 0.8113 (t0) cc_final: 0.7864 (t0) REVERT: E 211 ASP cc_start: 0.8283 (t0) cc_final: 0.7881 (t0) REVERT: E 297 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8077 (tm-30) REVERT: F 41 ASP cc_start: 0.7518 (p0) cc_final: 0.7278 (p0) REVERT: F 47 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7785 (mm-30) REVERT: F 137 LEU cc_start: 0.8809 (tt) cc_final: 0.8486 (tp) REVERT: F 138 THR cc_start: 0.8922 (m) cc_final: 0.8586 (p) REVERT: F 174 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8314 (p) REVERT: F 235 MET cc_start: 0.8142 (mtm) cc_final: 0.7764 (mtp) REVERT: F 299 LYS cc_start: 0.8806 (tttp) cc_final: 0.8571 (tmtt) REVERT: F 332 MET cc_start: 0.8916 (mmp) cc_final: 0.8691 (mmp) REVERT: N 95 LYS cc_start: 0.7749 (mttm) cc_final: 0.7054 (mmpt) REVERT: N 100 LYS cc_start: 0.5000 (mmtp) cc_final: 0.4216 (ptmt) REVERT: J 172 TYR cc_start: 0.8782 (t80) cc_final: 0.8553 (t80) REVERT: J 297 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7398 (tm-30) REVERT: J 352 LYS cc_start: 0.8433 (tttm) cc_final: 0.7960 (tppt) REVERT: J 413 MET cc_start: 0.8023 (ttm) cc_final: 0.7749 (ttm) REVERT: J 425 MET cc_start: 0.8684 (tpp) cc_final: 0.8185 (tpp) REVERT: J 431 ASP cc_start: 0.7541 (m-30) cc_final: 0.7247 (m-30) REVERT: G 47 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7557 (mm-30) REVERT: G 138 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8426 (p) REVERT: G 269 MET cc_start: 0.8431 (mtm) cc_final: 0.8050 (mtp) REVERT: G 323 MET cc_start: 0.8619 (ptp) cc_final: 0.8308 (ptp) REVERT: G 332 MET cc_start: 0.9134 (mmt) cc_final: 0.8887 (mmm) REVERT: G 393 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7847 (mm-30) REVERT: C 120 ASP cc_start: 0.8135 (m-30) cc_final: 0.7791 (m-30) REVERT: C 205 ASP cc_start: 0.8179 (t0) cc_final: 0.7796 (t0) REVERT: D 37 HIS cc_start: 0.7707 (m90) cc_final: 0.7457 (m90) REVERT: D 69 ASP cc_start: 0.7795 (t0) cc_final: 0.7552 (t0) REVERT: D 101 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8333 (t0) REVERT: D 373 MET cc_start: 0.8054 (ttp) cc_final: 0.7642 (ttp) REVERT: L 127 ASP cc_start: 0.8131 (m-30) cc_final: 0.7702 (m-30) REVERT: L 275 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8685 (p) REVERT: L 431 ASP cc_start: 0.7760 (m-30) cc_final: 0.7517 (m-30) REVERT: I 59 ASN cc_start: 0.8571 (m-40) cc_final: 0.8105 (p0) REVERT: I 123 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8156 (mtm180) REVERT: A 120 ASP cc_start: 0.8115 (m-30) cc_final: 0.7888 (m-30) REVERT: A 183 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7621 (mt-10) REVERT: A 211 ASP cc_start: 0.8155 (t0) cc_final: 0.7839 (t0) REVERT: A 382 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8982 (p) REVERT: B 278 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8363 (mmm160) REVERT: M 32 TYR cc_start: 0.7085 (m-10) cc_final: 0.6783 (m-80) REVERT: M 37 GLN cc_start: 0.7331 (mp10) cc_final: 0.7093 (mp10) REVERT: M 48 MET cc_start: 0.6125 (ttp) cc_final: 0.5626 (tmm) REVERT: M 95 LYS cc_start: 0.7424 (mttm) cc_final: 0.6845 (mmtt) REVERT: M 96 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5954 (mp) REVERT: M 100 LYS cc_start: 0.5126 (mmtp) cc_final: 0.4659 (ptmt) REVERT: H 26 ASP cc_start: 0.8307 (t0) cc_final: 0.7973 (t0) REVERT: H 212 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8867 (mp) REVERT: H 349 ASN cc_start: 0.8340 (m-40) cc_final: 0.7724 (t0) REVERT: H 435 TYR cc_start: 0.8548 (m-80) cc_final: 0.8339 (m-10) outliers start: 106 outliers final: 88 residues processed: 536 average time/residue: 0.2080 time to fit residues: 186.7313 Evaluate side-chains 532 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 437 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 118 ASN Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 349 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 431 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 378 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN K 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074209 restraints weight = 90250.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076804 restraints weight = 41296.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078561 restraints weight = 24587.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079750 restraints weight = 17162.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080562 restraints weight = 13343.385| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43998 Z= 0.122 Angle : 0.546 10.946 59746 Z= 0.277 Chirality : 0.042 0.175 6522 Planarity : 0.004 0.046 7776 Dihedral : 10.988 178.461 6142 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.19 % Allowed : 16.76 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.11), residues: 5388 helix: 2.17 (0.10), residues: 2546 sheet: 0.33 (0.18), residues: 768 loop : -0.55 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 278 TYR 0.026 0.001 TYR K 24 PHE 0.021 0.001 PHE I 377 TRP 0.015 0.001 TRP E 346 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00274 (43998) covalent geometry : angle 0.54641 (59746) hydrogen bonds : bond 0.04173 ( 2206) hydrogen bonds : angle 4.48881 ( 6408) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 447 time to evaluate : 1.095 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: E 120 ASP cc_start: 0.8173 (m-30) cc_final: 0.7829 (m-30) REVERT: E 127 ASP cc_start: 0.8532 (m-30) cc_final: 0.7872 (t0) REVERT: E 205 ASP cc_start: 0.8081 (t0) cc_final: 0.7819 (t0) REVERT: E 211 ASP cc_start: 0.8273 (t0) cc_final: 0.7877 (t0) REVERT: E 297 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8115 (tm-30) REVERT: F 41 ASP cc_start: 0.7519 (p0) cc_final: 0.7282 (p0) REVERT: F 47 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7780 (mm-30) REVERT: F 137 LEU cc_start: 0.8793 (tt) cc_final: 0.8473 (tp) REVERT: F 138 THR cc_start: 0.8911 (m) cc_final: 0.8587 (p) REVERT: F 174 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8268 (p) REVERT: F 235 MET cc_start: 0.8100 (mtm) cc_final: 0.7736 (mtp) REVERT: F 332 MET cc_start: 0.8913 (mmp) cc_final: 0.8696 (mmp) REVERT: N 95 LYS cc_start: 0.7747 (mttm) cc_final: 0.7063 (mmpt) REVERT: N 100 LYS cc_start: 0.4973 (mmtp) cc_final: 0.4211 (ptmt) REVERT: J 127 ASP cc_start: 0.8313 (m-30) cc_final: 0.7795 (m-30) REVERT: J 172 TYR cc_start: 0.8794 (t80) cc_final: 0.8542 (t80) REVERT: J 297 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7420 (tm-30) REVERT: J 413 MET cc_start: 0.7934 (ttm) cc_final: 0.7669 (ttm) REVERT: J 425 MET cc_start: 0.8680 (tpp) cc_final: 0.8197 (tpp) REVERT: J 431 ASP cc_start: 0.7500 (m-30) cc_final: 0.7202 (m-30) REVERT: G 47 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7557 (mm-30) REVERT: G 138 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8459 (p) REVERT: G 170 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8696 (p) REVERT: G 269 MET cc_start: 0.8439 (mtm) cc_final: 0.8040 (mtp) REVERT: G 323 MET cc_start: 0.8603 (ptp) cc_final: 0.8291 (ptp) REVERT: G 332 MET cc_start: 0.9122 (mmt) cc_final: 0.8861 (mmm) REVERT: G 393 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7777 (mm-30) REVERT: C 120 ASP cc_start: 0.8180 (m-30) cc_final: 0.7826 (m-30) REVERT: C 205 ASP cc_start: 0.8054 (t0) cc_final: 0.7665 (t0) REVERT: D 37 HIS cc_start: 0.7714 (m90) cc_final: 0.7454 (m90) REVERT: D 69 ASP cc_start: 0.7818 (t0) cc_final: 0.7609 (t0) REVERT: D 101 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8213 (t0) REVERT: D 373 MET cc_start: 0.8049 (ttp) cc_final: 0.7639 (ttp) REVERT: L 127 ASP cc_start: 0.8124 (m-30) cc_final: 0.7704 (m-30) REVERT: L 275 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8684 (p) REVERT: L 297 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7763 (tm-30) REVERT: I 59 ASN cc_start: 0.8566 (m-40) cc_final: 0.8109 (p0) REVERT: I 123 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8243 (mtm180) REVERT: A 120 ASP cc_start: 0.8109 (m-30) cc_final: 0.7895 (m-30) REVERT: A 127 ASP cc_start: 0.8710 (m-30) cc_final: 0.8257 (m-30) REVERT: A 183 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 211 ASP cc_start: 0.8149 (t0) cc_final: 0.7847 (t0) REVERT: B 278 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8367 (mmm160) REVERT: M 32 TYR cc_start: 0.7157 (m-10) cc_final: 0.6808 (m-80) REVERT: M 37 GLN cc_start: 0.7323 (mp10) cc_final: 0.7096 (mp10) REVERT: M 48 MET cc_start: 0.6059 (ttp) cc_final: 0.5848 (tmm) REVERT: M 95 LYS cc_start: 0.7409 (mttm) cc_final: 0.6834 (mmtt) REVERT: M 96 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5946 (mp) REVERT: M 100 LYS cc_start: 0.5222 (mmtp) cc_final: 0.4763 (ptmt) REVERT: K 18 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8171 (m110) REVERT: H 26 ASP cc_start: 0.8302 (t0) cc_final: 0.7941 (t0) REVERT: H 349 ASN cc_start: 0.8347 (m-40) cc_final: 0.7732 (t0) outliers start: 101 outliers final: 81 residues processed: 525 average time/residue: 0.2032 time to fit residues: 179.7543 Evaluate side-chains 516 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 428 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 222 optimal weight: 0.1980 chunk 449 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 476 optimal weight: 0.8980 chunk 331 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 443 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 469 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 118 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN K 61 HIS K 107 HIS K 128 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073456 restraints weight = 91221.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076022 restraints weight = 41589.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077759 restraints weight = 24746.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078924 restraints weight = 17272.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079725 restraints weight = 13456.861| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43998 Z= 0.157 Angle : 0.559 10.109 59746 Z= 0.285 Chirality : 0.042 0.171 6522 Planarity : 0.004 0.046 7776 Dihedral : 11.021 179.889 6141 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.23 % Allowed : 16.83 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.11), residues: 5388 helix: 2.17 (0.10), residues: 2544 sheet: 0.43 (0.18), residues: 738 loop : -0.57 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 278 TYR 0.024 0.001 TYR K 24 PHE 0.019 0.001 PHE I 262 TRP 0.014 0.001 TRP E 346 HIS 0.003 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00359 (43998) covalent geometry : angle 0.55922 (59746) hydrogen bonds : bond 0.04314 ( 2206) hydrogen bonds : angle 4.52433 ( 6408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6840.20 seconds wall clock time: 119 minutes 27.03 seconds (7167.03 seconds total)