Starting phenix.real_space_refine on Tue Sep 15 18:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jal_6350/09_2026/3jal_6350.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jal_6350/09_2026/3jal_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_6350/09_2026/3jal_6350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jal_6350/09_2026/3jal_6350.map" model { file = "/net/cci-nas-00/data/ceres_data/3jal_6350/09_2026/3jal_6350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jal_6350/09_2026/3jal_6350.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/3jal_6350/09_2026/3jal_6350.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jal_6350/09_2026/3jal_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1 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: 1 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: 1 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: 1 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: 1 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: 1 Time building chain proxies: 8.31, per 1000 atoms: 0.19 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: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.08 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: 10.59 Time building geometry restraints manager: 4.54 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: 25335 33.88 - 67.76: 725 67.76 - 101.64: 29 101.64 - 135.52: 1 135.52 - 169.40: 18 Dihedral angle restraints: 26108 sinusoidal: 10404 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 26105 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: 0.14 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: 12.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.790 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 : 15.763 169.404 16028 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 are 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/Z covalent geometry : bond 0.00897 / 0.62 (43998) covalent geometry : angle 1.45672 / 0.99 (59746) hydrogen bonds : bond 0.18646 / 12.60 ( 2206) hydrogen bonds : angle 7.16484 / 5.41 ( 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 : 1.412 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: 0.8796 (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: 0.7791 (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: 0.8320 (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: 0.2645 time to fit residues: 430.9249 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 : 1.573 ------------------------------------------------------------------------------- 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... 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 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 309 HIS 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 256 GLN ** 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 Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.092520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076931 restraints weight = 87908.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079680 restraints weight = 39918.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081453 restraints weight = 23614.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082725 restraints weight = 16615.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083559 restraints weight = 12843.429| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2534 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= 0.147 Angle : 0.592 7.260 59746 Z= 0.319 Chirality : 0.043 0.170 6522 Planarity : 0.005 0.051 7776 Dihedral : 11.047 175.271 6018 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.71 % Allowed : 11.17 % Favored : 87.12 % 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 are not related in a simple way. whole: 1.42 (0.11), residues: 5388 helix: 2.38 (0.10), residues: 2438 sheet: 0.69 (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 0.019 0.001 TYR J 24 PHE 0.021 0.002 PHE L 267 TRP 0.012 0.002 TRP C 346 HIS 0.008 0.001 HIS H 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (43998) covalent geometry : angle 0.59241 / 0.32 (59746) hydrogen bonds : bond 0.05959 / 4.02 ( 2206) hydrogen bonds : angle 5.08943 / 3.78 ( 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 676 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 597 time to evaluate : 1.559 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: 0.8064 (mm-30) cc_final: 0.7800 (mm-30) REVERT: E 120 ASP cc_start: 0.8228 (m-30) cc_final: 0.7959 (m-30) REVERT: E 154 MET cc_start: 0.9260 (mmm) cc_final: 0.8253 (mmt) REVERT: E 205 ASP cc_start: 0.8082 (t0) cc_final: 0.7850 (t0) REVERT: E 211 ASP cc_start: 0.8158 (t0) cc_final: 0.7909 (t0) REVERT: E 297 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 302 MET cc_start: 0.7788 (mtt) cc_final: 0.7384 (mtt) REVERT: F 269 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7866 (mtm) REVERT: F 393 GLU cc_start: 0.7950 (tp30) cc_final: 0.7744 (tp30) REVERT: N 32 TYR cc_start: 0.6654 (m-10) cc_final: 0.6116 (m-80) REVERT: J 297 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7589 (tm-30) REVERT: J 302 MET cc_start: 0.7212 (mtt) cc_final: 0.6913 (mtt) REVERT: J 352 LYS cc_start: 0.8227 (tttm) cc_final: 0.7732 (tppt) REVERT: J 398 MET cc_start: 0.8946 (mtp) cc_final: 0.8744 (mtm) REVERT: G 47 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7401 (mm-30) REVERT: G 59 ASN cc_start: 0.8672 (m110) cc_final: 0.7937 (p0) REVERT: G 75 MET cc_start: 0.9146 (mmt) cc_final: 0.8499 (mmt) REVERT: G 183 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: G 269 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8209 (mtm) REVERT: G 299 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7916 (ttpt) REVERT: G 323 MET cc_start: 0.8879 (ptp) cc_final: 0.8533 (ptp) REVERT: C 120 ASP cc_start: 0.8222 (m-30) cc_final: 0.7996 (m-30) REVERT: C 172 TYR cc_start: 0.8878 (t80) cc_final: 0.8565 (t80) REVERT: C 205 ASP cc_start: 0.8079 (t0) cc_final: 0.7836 (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: 0.8401 (tm-30) cc_final: 0.8044 (tm-30) REVERT: D 202 TYR cc_start: 0.8590 (m-80) cc_final: 0.8374 (m-80) REVERT: D 299 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7991 (tttp) REVERT: L 24 TYR cc_start: 0.8916 (m-80) cc_final: 0.8623 (m-80) REVERT: L 90 GLU cc_start: 0.8003 (mp0) cc_final: 0.7763 (mp0) REVERT: L 256 GLN cc_start: 0.8588 (pt0) cc_final: 0.7609 (tm-30) REVERT: L 284 GLU cc_start: 0.8137 (pt0) cc_final: 0.7649 (pm20) REVERT: I 59 ASN cc_start: 0.8536 (m110) cc_final: 0.7926 (p0) REVERT: I 161 TYR cc_start: 0.8455 (m-80) cc_final: 0.8231 (m-80) REVERT: I 200 GLU cc_start: 0.7858 (pt0) cc_final: 0.7624 (pt0) REVERT: I 299 LYS cc_start: 0.8416 (ptmt) cc_final: 0.8104 (tttp) REVERT: I 301 MET cc_start: 0.8492 (mmp) cc_final: 0.8292 (mmp) REVERT: A 154 MET cc_start: 0.9041 (mmm) cc_final: 0.7846 (mmt) REVERT: A 168 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7791 (mp0) REVERT: A 172 TYR cc_start: 0.8815 (t80) cc_final: 0.8594 (t80) REVERT: A 183 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7365 (mt-10) REVERT: B 41 ASP cc_start: 0.6873 (p0) cc_final: 0.6647 (p0) REVERT: B 202 TYR cc_start: 0.8781 (m-80) cc_final: 0.8417 (m-10) REVERT: M 20 MET cc_start: 0.6984 (ttp) cc_final: 0.6438 (mtt) REVERT: M 32 TYR cc_start: 0.7001 (m-10) cc_final: 0.6522 (m-80) REVERT: M 100 LYS cc_start: 0.5685 (mmtp) cc_final: 0.4864 (ptmt) REVERT: K 186 ASN cc_start: 0.8935 (m-40) cc_final: 0.8693 (m110) REVERT: K 253 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8680 (m) REVERT: K 413 MET cc_start: 0.7690 (ttm) cc_final: 0.7377 (ttm) REVERT: K 425 MET cc_start: 0.8310 (tpp) cc_final: 0.7875 (tpp) REVERT: K 431 ASP cc_start: 0.7508 (m-30) cc_final: 0.7216 (m-30) REVERT: H 47 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7615 (mm-30) REVERT: H 59 ASN cc_start: 0.8570 (m110) cc_final: 0.8097 (p0) REVERT: H 205 ASP cc_start: 0.8109 (t0) cc_final: 0.7827 (t0) REVERT: H 349 ASN cc_start: 0.7869 (m-40) cc_final: 0.7315 (t0) outliers start: 79 outliers final: 37 residues processed: 657 average time/residue: 0.2463 time to fit residues: 270.4417 Evaluate side-chains 516 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 474 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 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 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 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 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: 9.9990 chunk 525 optimal weight: 7.9990 chunk 374 optimal weight: 2.9990 chunk 440 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 338 optimal weight: 0.9980 chunk 512 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 8 HIS E 88 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS F 258 ASN F 293 GLN F 406 HIS N 104 ASN J 8 HIS J 28 HIS J 88 HIS J 283 HIS G 101 ASN G 139 HIS G 229 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 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 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073239 restraints weight = 89982.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075871 restraints weight = 42134.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077669 restraints weight = 25645.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078882 restraints weight = 18219.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079702 restraints weight = 14394.153| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3129 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= 0.200 Angle : 0.573 13.167 59746 Z= 0.302 Chirality : 0.044 0.154 6522 Planarity : 0.005 0.056 7776 Dihedral : 10.736 179.837 6005 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.66 % Allowed : 12.69 % Favored : 84.65 % 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 are not related in a simple way. whole: 1.38 (0.11), residues: 5388 helix: 2.33 (0.10), residues: 2460 sheet: 0.59 (0.18), residues: 756 loop : -0.64 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 278 TYR 0.027 0.001 TYR K 24 PHE 0.020 0.002 PHE B 296 TRP 0.012 0.002 TRP K 346 HIS 0.008 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (43998) covalent geometry : angle 0.57293 / 0.30 (59746) hydrogen bonds : bond 0.05365 / 3.62 ( 2206) hydrogen bonds : angle 4.81802 / 3.56 ( 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 599 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 476 time to evaluate : 1.571 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: 0.8086 (mm-30) cc_final: 0.7866 (mm-30) REVERT: E 120 ASP cc_start: 0.8245 (m-30) cc_final: 0.7976 (m-30) REVERT: E 154 MET cc_start: 0.9057 (mmm) cc_final: 0.8763 (mmp) REVERT: E 205 ASP cc_start: 0.8205 (t0) cc_final: 0.7948 (t0) REVERT: E 211 ASP cc_start: 0.8273 (t0) cc_final: 0.7930 (t0) REVERT: E 302 MET cc_start: 0.7940 (mtt) cc_final: 0.7328 (mtt) REVERT: F 26 ASP cc_start: 0.8305 (t0) cc_final: 0.8049 (t0) REVERT: F 332 MET cc_start: 0.8852 (mmp) cc_final: 0.8638 (mmp) REVERT: N 32 TYR cc_start: 0.6764 (m-10) cc_final: 0.6531 (m-80) REVERT: N 100 LYS cc_start: 0.4788 (mmtp) cc_final: 0.4015 (ptmt) REVERT: J 297 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7407 (tm-30) REVERT: J 302 MET cc_start: 0.7749 (mtt) cc_final: 0.7428 (mtt) REVERT: G 47 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7436 (mm-30) REVERT: G 75 MET cc_start: 0.9145 (mmt) cc_final: 0.8448 (mmt) REVERT: G 269 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8135 (mtp) REVERT: G 323 MET cc_start: 0.8795 (ptp) cc_final: 0.8014 (ptp) REVERT: C 120 ASP cc_start: 0.8169 (m-30) cc_final: 0.7915 (m-30) REVERT: C 123 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8329 (tpp80) REVERT: C 205 ASP cc_start: 0.8203 (t0) cc_final: 0.7912 (t0) REVERT: C 285 GLN cc_start: 0.8175 (pt0) cc_final: 0.7549 (mm110) REVERT: C 309 HIS cc_start: 0.7607 (m90) cc_final: 0.7211 (m90) REVERT: C 425 MET cc_start: 0.8650 (tpp) cc_final: 0.8369 (tpp) REVERT: D 299 LYS cc_start: 0.8578 (ptmt) cc_final: 0.8188 (tttp) REVERT: L 24 TYR cc_start: 0.8960 (m-80) cc_final: 0.8663 (m-80) REVERT: L 127 ASP cc_start: 0.8195 (m-30) cc_final: 0.7854 (m-30) REVERT: L 284 GLU cc_start: 0.8162 (pt0) cc_final: 0.7662 (pm20) REVERT: I 145 THR cc_start: 0.8769 (m) cc_final: 0.8385 (p) REVERT: I 200 GLU cc_start: 0.8001 (pt0) cc_final: 0.7732 (pt0) REVERT: I 205 ASP cc_start: 0.8421 (t0) cc_final: 0.8215 (t0) REVERT: I 299 LYS cc_start: 0.8541 (ptmt) cc_final: 0.8280 (tttp) REVERT: I 301 MET cc_start: 0.8567 (mmp) cc_final: 0.8301 (mmp) REVERT: A 154 MET cc_start: 0.8909 (mmm) cc_final: 0.8339 (mmm) REVERT: A 183 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 211 ASP cc_start: 0.8296 (t0) cc_final: 0.8055 (t0) REVERT: A 297 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 382 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8701 (p) REVERT: M 32 TYR cc_start: 0.6960 (m-10) cc_final: 0.6337 (m-80) REVERT: M 95 LYS cc_start: 0.7294 (mttm) cc_final: 0.6674 (mmtt) REVERT: M 100 LYS cc_start: 0.5404 (mmtp) cc_final: 0.4811 (ptmt) REVERT: H 26 ASP cc_start: 0.8321 (t0) cc_final: 0.7914 (t0) REVERT: H 47 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7507 (mm-30) REVERT: H 59 ASN cc_start: 0.8647 (m110) cc_final: 0.8250 (p0) REVERT: H 240 THR cc_start: 0.9301 (t) cc_final: 0.8947 (m) REVERT: H 254 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8447 (ttpt) REVERT: H 349 ASN cc_start: 0.8103 (m-40) cc_final: 0.7583 (t0) outliers start: 123 outliers final: 66 residues processed: 569 average time/residue: 0.2449 time to fit residues: 233.8915 Evaluate side-chains 505 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 436 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 F residue 114 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 381 SER 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 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 12 CYS Chi-restraints excluded: chain G residue 114 LEU 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 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 269 MET Chi-restraints excluded: chain D residue 373 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 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 241 CYS Chi-restraints excluded: chain I residue 269 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 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 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 194 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: 3.9990 chunk 458 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 292 optimal weight: 2.9990 chunk 493 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 88 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 433 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN K 283 HIS H 107 HIS H 436 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072522 restraints weight = 90514.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075143 restraints weight = 41999.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076954 restraints weight = 25571.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078119 restraints weight = 18202.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078956 restraints weight = 14456.586| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 43998 Z= 0.176 Angle : 0.542 11.848 59746 Z= 0.284 Chirality : 0.043 0.153 6522 Planarity : 0.004 0.049 7776 Dihedral : 10.655 178.106 6002 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.62 % Allowed : 13.25 % Favored : 84.13 % 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 are not related in a simple way. whole: 1.30 (0.11), residues: 5388 helix: 2.23 (0.10), residues: 2498 sheet: 0.55 (0.18), residues: 768 loop : -0.70 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 339 TYR 0.019 0.001 TYR K 24 PHE 0.021 0.001 PHE N 107 TRP 0.012 0.001 TRP E 346 HIS 0.006 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (43998) covalent geometry : angle 0.54190 / 0.28 (59746) hydrogen bonds : bond 0.04972 / 3.36 ( 2206) hydrogen bonds : angle 4.69439 / 3.46 ( 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 590 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 469 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7879 (mm-30) REVERT: E 120 ASP cc_start: 0.8220 (m-30) cc_final: 0.7933 (m-30) REVERT: E 154 MET cc_start: 0.9251 (mmm) cc_final: 0.8729 (mmp) REVERT: E 205 ASP cc_start: 0.8192 (t0) cc_final: 0.7930 (t0) REVERT: E 211 ASP cc_start: 0.8246 (t0) cc_final: 0.7874 (t0) REVERT: E 339 ARG cc_start: 0.8169 (ptt-90) cc_final: 0.7732 (ptt180) REVERT: F 26 ASP cc_start: 0.8373 (t0) cc_final: 0.8090 (t0) REVERT: F 138 THR cc_start: 0.9069 (m) cc_final: 0.8520 (p) REVERT: F 200 GLU cc_start: 0.8041 (pt0) cc_final: 0.7733 (pt0) REVERT: F 235 MET cc_start: 0.8243 (mtm) cc_final: 0.7701 (mtp) REVERT: F 254 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8578 (mtmt) REVERT: F 269 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7990 (mtm) REVERT: F 332 MET cc_start: 0.8871 (mmp) cc_final: 0.8644 (mmp) REVERT: N 35 ILE cc_start: 0.7972 (mp) cc_final: 0.7591 (mt) REVERT: N 95 LYS cc_start: 0.7589 (mttm) cc_final: 0.6762 (mtmt) REVERT: N 100 LYS cc_start: 0.4806 (mmtp) cc_final: 0.4029 (ptmt) REVERT: J 36 MET cc_start: 0.8389 (ptm) cc_final: 0.8186 (ptm) REVERT: J 297 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7399 (tm-30) REVERT: J 302 MET cc_start: 0.7936 (mtt) cc_final: 0.7571 (ttm) REVERT: J 377 MET cc_start: 0.8545 (ttp) cc_final: 0.8318 (ttp) REVERT: G 47 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7560 (mm-30) REVERT: G 75 MET cc_start: 0.9148 (mmt) cc_final: 0.8520 (mmt) REVERT: G 323 MET cc_start: 0.8752 (ptp) cc_final: 0.8052 (ptp) REVERT: C 120 ASP cc_start: 0.8135 (m-30) cc_final: 0.7790 (m-30) REVERT: C 205 ASP cc_start: 0.8299 (t0) cc_final: 0.7964 (t0) REVERT: C 269 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8842 (pp) REVERT: C 425 MET cc_start: 0.8710 (tpp) cc_final: 0.8434 (tpp) REVERT: D 299 LYS cc_start: 0.8486 (ptmt) cc_final: 0.8139 (tttp) REVERT: L 127 ASP cc_start: 0.8209 (m-30) cc_final: 0.7907 (m-30) REVERT: L 284 GLU cc_start: 0.8119 (pt0) cc_final: 0.7620 (pm20) REVERT: I 59 ASN cc_start: 0.8554 (m-40) cc_final: 0.7983 (p0) REVERT: I 123 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8198 (mtm180) REVERT: I 145 THR cc_start: 0.8669 (m) cc_final: 0.8391 (p) REVERT: I 200 GLU cc_start: 0.7986 (pt0) cc_final: 0.7599 (pt0) REVERT: I 299 LYS cc_start: 0.8588 (ptmt) cc_final: 0.8370 (tttp) REVERT: I 301 MET cc_start: 0.8583 (mmp) cc_final: 0.8293 (mmp) REVERT: A 127 ASP cc_start: 0.8722 (m-30) cc_final: 0.8314 (m-30) REVERT: A 154 MET cc_start: 0.8916 (mmm) cc_final: 0.8398 (mmm) REVERT: A 183 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 211 ASP cc_start: 0.8245 (t0) cc_final: 0.7968 (t0) REVERT: A 253 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8731 (m) REVERT: A 297 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 309 HIS cc_start: 0.7472 (m90) cc_final: 0.6878 (m90) REVERT: A 382 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8701 (p) REVERT: M 32 TYR cc_start: 0.6830 (m-10) cc_final: 0.6343 (m-80) REVERT: M 34 LYS cc_start: 0.7238 (mmmt) cc_final: 0.6772 (mppt) REVERT: M 37 GLN cc_start: 0.6925 (mp10) cc_final: 0.6456 (mp10) REVERT: M 48 MET cc_start: 0.6196 (ttp) cc_final: 0.5744 (tmm) REVERT: M 95 LYS cc_start: 0.7344 (mttm) cc_final: 0.6727 (mmtt) REVERT: M 96 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5845 (mp) REVERT: M 100 LYS cc_start: 0.5279 (mmtp) cc_final: 0.4665 (ptmt) REVERT: K 90 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: K 123 ARG cc_start: 0.8495 (tpp-160) cc_final: 0.8031 (tpp80) REVERT: K 172 TYR cc_start: 0.8893 (t80) cc_final: 0.8447 (t80) REVERT: K 425 MET cc_start: 0.8555 (tpp) cc_final: 0.8312 (tpp) REVERT: K 431 ASP cc_start: 0.7538 (m-30) cc_final: 0.7324 (m-30) REVERT: H 26 ASP cc_start: 0.8400 (t0) cc_final: 0.8025 (t0) REVERT: H 47 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7547 (mm-30) REVERT: H 205 ASP cc_start: 0.8158 (t0) cc_final: 0.7882 (t0) REVERT: H 254 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8441 (ttpt) REVERT: H 269 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8186 (ptp) REVERT: H 299 LYS cc_start: 0.8674 (ptmt) cc_final: 0.8411 (tttp) REVERT: H 349 ASN cc_start: 0.8179 (m-40) cc_final: 0.7716 (t0) outliers start: 121 outliers final: 75 residues processed: 558 average time/residue: 0.2484 time to fit residues: 232.1055 Evaluate side-chains 510 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 426 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 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 254 LYS Chi-restraints excluded: chain F residue 269 MET 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 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 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 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 C residue 54 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 269 LEU 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 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 213 CYS 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 4 ILE 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 172 VAL 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 96 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 90 GLU 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 93 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 269 MET 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: 4.9990 chunk 296 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 357 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 531 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 339 optimal weight: 0.0870 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN E 88 HIS E 107 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN N 118 ASN D 229 HIS D 331 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 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** B 281 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073798 restraints weight = 89969.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076465 restraints weight = 41884.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078280 restraints weight = 25407.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079483 restraints weight = 18066.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.080322 restraints weight = 14278.730| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43998 Z= 0.122 Angle : 0.513 12.890 59746 Z= 0.265 Chirality : 0.042 0.147 6522 Planarity : 0.004 0.047 7776 Dihedral : 10.521 178.649 6001 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.51 % Allowed : 13.82 % Favored : 83.67 % 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 are not related in a simple way. whole: 1.37 (0.11), residues: 5388 helix: 2.31 (0.10), residues: 2498 sheet: 0.53 (0.18), residues: 780 loop : -0.67 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 308 TYR 0.031 0.001 TYR K 24 PHE 0.015 0.001 PHE N 107 TRP 0.013 0.001 TRP E 346 HIS 0.008 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (43998) covalent geometry : angle 0.51284 / 0.26 (59746) hydrogen bonds : bond 0.04456 / 3.02 ( 2206) hydrogen bonds : angle 4.54745 / 3.34 ( 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 607 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 491 time to evaluate : 1.602 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: 0.8104 (mm-30) cc_final: 0.7891 (mm-30) REVERT: E 120 ASP cc_start: 0.8118 (m-30) cc_final: 0.7814 (m-30) REVERT: E 154 MET cc_start: 0.9188 (mmm) cc_final: 0.8784 (mmp) REVERT: E 205 ASP cc_start: 0.8148 (t0) cc_final: 0.7846 (t0) REVERT: E 211 ASP cc_start: 0.8239 (t0) cc_final: 0.7853 (t0) REVERT: E 297 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7933 (tm-30) REVERT: F 26 ASP cc_start: 0.8378 (t0) cc_final: 0.8052 (t0) REVERT: F 138 THR cc_start: 0.8902 (m) cc_final: 0.8630 (p) REVERT: F 235 MET cc_start: 0.8116 (mtm) cc_final: 0.7773 (mtp) REVERT: F 254 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8574 (mtmt) REVERT: F 269 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8051 (mtm) REVERT: F 332 MET cc_start: 0.8870 (mmp) cc_final: 0.8664 (mmp) REVERT: N 95 LYS cc_start: 0.7579 (mttm) cc_final: 0.6792 (mtmt) REVERT: N 100 LYS cc_start: 0.4724 (mmtp) cc_final: 0.4052 (ptmt) REVERT: J 36 MET cc_start: 0.8398 (ptm) cc_final: 0.8180 (ptm) REVERT: J 297 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7384 (tm-30) REVERT: J 302 MET cc_start: 0.7859 (mtt) cc_final: 0.7547 (ttm) REVERT: J 352 LYS cc_start: 0.8291 (tttm) cc_final: 0.7956 (tppt) REVERT: J 425 MET cc_start: 0.8604 (tpp) cc_final: 0.8133 (tpp) REVERT: G 47 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7512 (mm-30) REVERT: G 75 MET cc_start: 0.9178 (mmt) cc_final: 0.8532 (mmt) REVERT: G 138 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8410 (p) REVERT: G 200 GLU cc_start: 0.8427 (pt0) cc_final: 0.8210 (pt0) REVERT: G 299 LYS cc_start: 0.8282 (tttp) cc_final: 0.7901 (tmtt) REVERT: G 323 MET cc_start: 0.8705 (ptp) cc_final: 0.8118 (ptp) REVERT: G 393 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 120 ASP cc_start: 0.8139 (m-30) cc_final: 0.7753 (m-30) REVERT: C 205 ASP cc_start: 0.8208 (t0) cc_final: 0.7771 (t0) REVERT: C 297 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7960 (tm-30) REVERT: C 425 MET cc_start: 0.8810 (tpp) cc_final: 0.8561 (tpp) REVERT: L 127 ASP cc_start: 0.8160 (m-30) cc_final: 0.7896 (m-30) REVERT: L 284 GLU cc_start: 0.8118 (pt0) cc_final: 0.7681 (pm20) REVERT: L 413 MET cc_start: 0.7786 (ttm) cc_final: 0.7559 (tpp) REVERT: L 431 ASP cc_start: 0.7837 (m-30) cc_final: 0.7583 (m-30) REVERT: I 59 ASN cc_start: 0.8448 (m-40) cc_final: 0.7940 (p0) REVERT: I 123 ARG cc_start: 0.8838 (ttm110) cc_final: 0.8251 (mtm180) REVERT: I 149 MET cc_start: 0.8915 (ttt) cc_final: 0.8696 (ttt) REVERT: I 200 GLU cc_start: 0.7852 (pt0) cc_final: 0.7505 (pt0) REVERT: I 299 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8365 (tttp) REVERT: I 301 MET cc_start: 0.8519 (mmp) cc_final: 0.8245 (mmp) REVERT: A 127 ASP cc_start: 0.8684 (m-30) cc_final: 0.8252 (m-30) REVERT: A 154 MET cc_start: 0.8908 (mmm) cc_final: 0.8402 (mmm) REVERT: A 382 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8780 (p) REVERT: B 138 THR cc_start: 0.8902 (m) cc_final: 0.8686 (p) REVERT: M 32 TYR cc_start: 0.7000 (m-10) cc_final: 0.6409 (m-80) REVERT: M 34 LYS cc_start: 0.7591 (mmmt) cc_final: 0.7104 (mppt) REVERT: M 37 GLN cc_start: 0.7100 (mp10) cc_final: 0.6680 (mp10) REVERT: M 48 MET cc_start: 0.5949 (ttp) cc_final: 0.5637 (tmm) REVERT: M 95 LYS cc_start: 0.7291 (mttm) cc_final: 0.6656 (mmtt) REVERT: M 96 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5867 (mp) REVERT: M 100 LYS cc_start: 0.5181 (mmtp) cc_final: 0.4659 (ptmt) REVERT: K 18 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.7963 (m110) REVERT: K 172 TYR cc_start: 0.8899 (t80) cc_final: 0.8464 (t80) REVERT: K 425 MET cc_start: 0.8642 (tpp) cc_final: 0.8397 (tpp) REVERT: H 26 ASP cc_start: 0.8348 (t0) cc_final: 0.7977 (t0) REVERT: H 205 ASP cc_start: 0.8108 (t0) cc_final: 0.7772 (t0) REVERT: H 240 THR cc_start: 0.9319 (t) cc_final: 0.8939 (m) REVERT: H 254 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8385 (ttpt) REVERT: H 349 ASN cc_start: 0.8278 (m-40) cc_final: 0.7762 (t0) REVERT: H 435 TYR cc_start: 0.8892 (m-80) cc_final: 0.8503 (m-80) outliers start: 116 outliers final: 70 residues processed: 580 average time/residue: 0.2397 time to fit residues: 233.5067 Evaluate side-chains 511 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 434 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER 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 114 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 254 LYS 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 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 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 138 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 170 SER 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 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 275 VAL Chi-restraints excluded: chain L residue 315 CYS 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 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 344 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 356 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 36 MET 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 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 213 CYS Chi-restraints excluded: chain H residue 254 LYS 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: 9.9990 chunk 85 optimal weight: 30.0000 chunk 249 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 464 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 392 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN E 88 HIS E 216 ASN E 283 HIS F 247 GLN F 433 GLN G 258 ASN D 247 GLN D 309 HIS ** 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** B 107 HIS B 247 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.069689 restraints weight = 92533.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072178 restraints weight = 43342.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.073920 restraints weight = 26582.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075035 restraints weight = 19004.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075834 restraints weight = 15170.390| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 43998 Z= 0.288 Angle : 0.624 11.083 59746 Z= 0.326 Chirality : 0.045 0.192 6522 Planarity : 0.005 0.050 7776 Dihedral : 10.744 179.479 6000 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.90 % Allowed : 14.83 % Favored : 82.27 % 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 are not related in a simple way. whole: 1.09 (0.11), residues: 5388 helix: 2.05 (0.10), residues: 2504 sheet: 0.42 (0.18), residues: 738 loop : -0.77 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG H 215 TYR 0.029 0.002 TYR L 24 PHE 0.018 0.002 PHE K 67 TRP 0.013 0.002 TRP K 346 HIS 0.006 0.001 HIS N 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.29 (43998) covalent geometry : angle 0.62366 / 0.33 (59746) hydrogen bonds : bond 0.05559 / 3.74 ( 2206) hydrogen bonds : angle 4.81562 / 3.52 ( 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 570 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 436 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8243 (m-30) cc_final: 0.7941 (m-30) REVERT: E 205 ASP cc_start: 0.8365 (t0) cc_final: 0.8056 (t0) REVERT: E 211 ASP cc_start: 0.8243 (t0) cc_final: 0.7889 (t0) REVERT: E 297 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 26 ASP cc_start: 0.8424 (t0) cc_final: 0.8149 (t0) REVERT: F 41 ASP cc_start: 0.7519 (p0) cc_final: 0.7199 (p0) REVERT: F 47 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7707 (mm-30) REVERT: F 235 MET cc_start: 0.8499 (mtm) cc_final: 0.7917 (mtp) REVERT: F 332 MET cc_start: 0.8870 (mmp) cc_final: 0.8636 (mmp) REVERT: N 35 ILE cc_start: 0.7950 (mp) cc_final: 0.7571 (mt) REVERT: N 95 LYS cc_start: 0.7636 (mttm) cc_final: 0.6830 (mtmt) REVERT: N 100 LYS cc_start: 0.4939 (mmtp) cc_final: 0.4168 (ptmt) REVERT: J 127 ASP cc_start: 0.8170 (m-30) cc_final: 0.7674 (m-30) REVERT: J 297 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7574 (tm-30) REVERT: J 302 MET cc_start: 0.8028 (mtt) cc_final: 0.7828 (ttm) REVERT: J 352 LYS cc_start: 0.8445 (tttm) cc_final: 0.8031 (tppt) REVERT: J 413 MET cc_start: 0.8208 (ttm) cc_final: 0.8000 (ttm) REVERT: G 47 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7555 (mm-30) REVERT: G 75 MET cc_start: 0.9044 (mmt) cc_final: 0.8502 (mmt) REVERT: G 113 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7776 (mm-30) REVERT: G 323 MET cc_start: 0.8761 (ptp) cc_final: 0.8030 (ptp) REVERT: G 393 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7870 (mm-30) REVERT: C 120 ASP cc_start: 0.8154 (m-30) cc_final: 0.7846 (m-30) REVERT: C 205 ASP cc_start: 0.8360 (t0) cc_final: 0.8008 (t0) REVERT: L 127 ASP cc_start: 0.8243 (m-30) cc_final: 0.7955 (m-30) REVERT: L 431 ASP cc_start: 0.7890 (m-30) cc_final: 0.7647 (m-30) REVERT: I 200 GLU cc_start: 0.7986 (pt0) cc_final: 0.7635 (pt0) REVERT: I 301 MET cc_start: 0.8620 (mmp) cc_final: 0.8372 (mmp) REVERT: A 154 MET cc_start: 0.8909 (mmm) cc_final: 0.8695 (mmm) REVERT: A 183 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 299 LYS cc_start: 0.8780 (ptmt) cc_final: 0.8470 (tttp) REVERT: M 32 TYR cc_start: 0.6987 (m-10) cc_final: 0.6552 (m-80) REVERT: M 34 LYS cc_start: 0.7322 (mmmt) cc_final: 0.7055 (mppt) REVERT: M 35 ILE cc_start: 0.7800 (mp) cc_final: 0.7338 (mt) REVERT: M 48 MET cc_start: 0.6105 (ttp) cc_final: 0.5721 (tmm) REVERT: M 95 LYS cc_start: 0.7467 (mttm) cc_final: 0.6924 (mmtt) REVERT: M 96 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5671 (mp) REVERT: M 100 LYS cc_start: 0.5264 (mmtp) cc_final: 0.4676 (ptmt) REVERT: K 425 MET cc_start: 0.8721 (tpp) cc_final: 0.8449 (tpp) REVERT: H 26 ASP cc_start: 0.8389 (t0) cc_final: 0.8021 (t0) REVERT: H 205 ASP cc_start: 0.8155 (t0) cc_final: 0.7931 (t0) REVERT: H 349 ASN cc_start: 0.8334 (m-40) cc_final: 0.7803 (t0) outliers start: 134 outliers final: 98 residues processed: 531 average time/residue: 0.2423 time to fit residues: 215.2774 Evaluate side-chains 506 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 407 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 115 ILE 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 E residue 363 VAL Chi-restraints excluded: chain F residue 25 SER 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 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 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 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 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 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 220 THR 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 335 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 36 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 288 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 338 LYS Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 170 SER 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 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 363 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 4 ILE 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 190 SER 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 96 LEU 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 381 THR 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 232 SER Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 269 MET 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: 0.7980 chunk 446 optimal weight: 0.5980 chunk 371 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 463 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 397 optimal weight: 3.9990 chunk 481 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN E 88 HIS N 118 ASN G 331 GLN C 18 ASN C 88 HIS D 107 HIS ** 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** ** K 88 HIS ** 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 = 0.3533 r_free = 0.3533 target = 0.089060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072897 restraints weight = 90107.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075522 restraints weight = 42210.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077312 restraints weight = 25720.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078470 restraints weight = 18349.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079282 restraints weight = 14618.066| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43998 Z= 0.122 Angle : 0.528 11.633 59746 Z= 0.271 Chirality : 0.041 0.148 6522 Planarity : 0.004 0.047 7776 Dihedral : 10.552 178.965 5995 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.32 % Allowed : 15.63 % Favored : 82.05 % 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 are not related in a simple way. whole: 1.30 (0.11), residues: 5388 helix: 2.25 (0.10), residues: 2504 sheet: 0.33 (0.18), residues: 768 loop : -0.64 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 278 TYR 0.023 0.001 TYR K 24 PHE 0.013 0.001 PHE E 135 TRP 0.015 0.001 TRP E 21 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (43998) covalent geometry : angle 0.52756 / 0.27 (59746) hydrogen bonds : bond 0.04400 / 2.98 ( 2206) hydrogen bonds : angle 4.52677 / 3.32 ( 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 569 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 462 time to evaluate : 1.676 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: 0.8150 (m-30) cc_final: 0.7833 (m-30) REVERT: E 205 ASP cc_start: 0.8201 (t0) cc_final: 0.7893 (t0) REVERT: E 211 ASP cc_start: 0.8303 (t0) cc_final: 0.7892 (t0) REVERT: E 297 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8106 (tm-30) REVERT: F 26 ASP cc_start: 0.8385 (t0) cc_final: 0.8033 (t0) REVERT: F 41 ASP cc_start: 0.7389 (p0) cc_final: 0.7157 (p0) REVERT: F 47 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7782 (mm-30) REVERT: F 137 LEU cc_start: 0.8793 (tt) cc_final: 0.8529 (tp) REVERT: F 138 THR cc_start: 0.8959 (m) cc_final: 0.8578 (p) REVERT: F 235 MET cc_start: 0.8073 (mtm) cc_final: 0.7624 (mtp) REVERT: F 254 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8566 (mtmt) REVERT: F 299 LYS cc_start: 0.8689 (tttp) cc_final: 0.8481 (tmtt) REVERT: F 332 MET cc_start: 0.8892 (mmp) cc_final: 0.8659 (mmp) REVERT: N 95 LYS cc_start: 0.7652 (mttm) cc_final: 0.6852 (mtmt) REVERT: N 100 LYS cc_start: 0.4814 (mmtp) cc_final: 0.4119 (ptmt) REVERT: J 172 TYR cc_start: 0.8633 (t80) cc_final: 0.8323 (t80) REVERT: J 297 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7430 (tm-30) REVERT: J 352 LYS cc_start: 0.8420 (tttm) cc_final: 0.8001 (tppt) REVERT: J 413 MET cc_start: 0.7977 (ttm) cc_final: 0.7739 (ttm) REVERT: J 425 MET cc_start: 0.8633 (tpp) cc_final: 0.8171 (tpp) REVERT: G 47 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7658 (mm-30) REVERT: G 71 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6877 (tm-30) REVERT: G 75 MET cc_start: 0.9107 (mmt) cc_final: 0.8527 (mmt) REVERT: G 393 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7843 (mm-30) REVERT: C 120 ASP cc_start: 0.8139 (m-30) cc_final: 0.7747 (m-30) REVERT: C 205 ASP cc_start: 0.8193 (t0) cc_final: 0.7821 (t0) REVERT: D 286 LEU cc_start: 0.8369 (pt) cc_final: 0.7903 (pp) REVERT: L 127 ASP cc_start: 0.8162 (m-30) cc_final: 0.7886 (m-30) REVERT: L 431 ASP cc_start: 0.7817 (m-30) cc_final: 0.7578 (m-30) REVERT: I 59 ASN cc_start: 0.8552 (m-40) cc_final: 0.8078 (p0) REVERT: I 123 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8154 (mtm180) REVERT: I 200 GLU cc_start: 0.7958 (pt0) cc_final: 0.7710 (pt0) REVERT: A 183 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 297 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 382 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8790 (p) REVERT: B 259 MET cc_start: 0.8967 (mmm) cc_final: 0.8658 (mmp) REVERT: B 278 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8315 (mmm160) REVERT: M 32 TYR cc_start: 0.7009 (m-10) cc_final: 0.6654 (m-80) REVERT: M 34 LYS cc_start: 0.7523 (mmmt) cc_final: 0.7018 (mppt) REVERT: M 35 ILE cc_start: 0.8029 (mp) cc_final: 0.7629 (mt) REVERT: M 37 GLN cc_start: 0.7090 (mp10) cc_final: 0.6718 (mp10) REVERT: M 48 MET cc_start: 0.6017 (ttp) cc_final: 0.5512 (tmm) REVERT: M 95 LYS cc_start: 0.7394 (mttm) cc_final: 0.6820 (mmtt) REVERT: M 96 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5818 (mp) REVERT: M 100 LYS cc_start: 0.5320 (mmtp) cc_final: 0.4670 (ptmt) REVERT: K 18 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.7961 (m110) REVERT: H 26 ASP cc_start: 0.8315 (t0) cc_final: 0.7991 (t0) REVERT: H 299 LYS cc_start: 0.8436 (tttp) cc_final: 0.8228 (tmtt) REVERT: H 349 ASN cc_start: 0.8339 (m-40) cc_final: 0.7745 (t0) REVERT: H 435 TYR cc_start: 0.8778 (m-80) cc_final: 0.8511 (m-10) outliers start: 107 outliers final: 69 residues processed: 545 average time/residue: 0.2435 time to fit residues: 221.1578 Evaluate side-chains 492 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 419 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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 E residue 344 VAL Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 254 LYS 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 415 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 130 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 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 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 279 GLU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 190 THR 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 241 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 286 LEU 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 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 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 213 CYS Chi-restraints excluded: chain H residue 286 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: 7.9990 chunk 73 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 438 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 358 optimal weight: 0.9990 chunk 306 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 88 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 436 GLN ** 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** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072643 restraints weight = 91138.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075270 restraints weight = 42628.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077052 restraints weight = 25931.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.078241 restraints weight = 18467.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079055 restraints weight = 14611.859| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43998 Z= 0.136 Angle : 0.537 10.386 59746 Z= 0.273 Chirality : 0.042 0.153 6522 Planarity : 0.004 0.047 7776 Dihedral : 10.518 179.469 5994 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.19 % Allowed : 15.85 % Favored : 81.96 % 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 are not related in a simple way. whole: 1.36 (0.11), residues: 5388 helix: 2.25 (0.10), residues: 2508 sheet: 0.46 (0.18), residues: 756 loop : -0.58 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 278 TYR 0.031 0.001 TYR K 24 PHE 0.014 0.001 PHE I 377 TRP 0.013 0.001 TRP E 21 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (43998) covalent geometry : angle 0.53679 / 0.27 (59746) hydrogen bonds : bond 0.04392 / 2.96 ( 2206) hydrogen bonds : angle 4.51884 / 3.31 ( 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 544 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 443 time to evaluate : 1.720 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: 0.8158 (m-30) cc_final: 0.7850 (m-30) REVERT: E 205 ASP cc_start: 0.8198 (t0) cc_final: 0.7908 (t0) REVERT: E 211 ASP cc_start: 0.8294 (t0) cc_final: 0.7888 (t0) REVERT: E 297 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8083 (tm-30) REVERT: F 26 ASP cc_start: 0.8394 (t0) cc_final: 0.8040 (t0) REVERT: F 41 ASP cc_start: 0.7411 (p0) cc_final: 0.7182 (p0) REVERT: F 47 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7840 (mm-30) REVERT: F 137 LEU cc_start: 0.8792 (tt) cc_final: 0.8522 (tp) REVERT: F 138 THR cc_start: 0.8963 (m) cc_final: 0.8589 (p) REVERT: F 235 MET cc_start: 0.8282 (mtm) cc_final: 0.7881 (mtp) REVERT: F 254 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8623 (mtmt) REVERT: F 299 LYS cc_start: 0.8724 (tttp) cc_final: 0.8487 (tmtt) REVERT: F 332 MET cc_start: 0.8888 (mmp) cc_final: 0.8663 (mmp) REVERT: N 95 LYS cc_start: 0.7665 (mttm) cc_final: 0.6865 (mtmt) REVERT: N 100 LYS cc_start: 0.5174 (mmtp) cc_final: 0.4393 (ptmt) REVERT: J 172 TYR cc_start: 0.8599 (t80) cc_final: 0.8298 (t80) REVERT: J 297 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7376 (tm-30) REVERT: J 352 LYS cc_start: 0.8476 (tttm) cc_final: 0.8054 (tppt) REVERT: J 413 MET cc_start: 0.8017 (ttm) cc_final: 0.7748 (ttm) REVERT: J 425 MET cc_start: 0.8630 (tpp) cc_final: 0.8184 (tpp) REVERT: G 47 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7577 (mm-30) REVERT: G 75 MET cc_start: 0.9116 (mmt) cc_final: 0.8680 (mmt) REVERT: G 393 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7854 (mm-30) REVERT: C 120 ASP cc_start: 0.8132 (m-30) cc_final: 0.7749 (m-30) REVERT: C 205 ASP cc_start: 0.8221 (t0) cc_final: 0.7847 (t0) REVERT: D 286 LEU cc_start: 0.8388 (pt) cc_final: 0.7918 (pp) REVERT: L 127 ASP cc_start: 0.8159 (m-30) cc_final: 0.7718 (m-30) REVERT: L 306 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8458 (t70) REVERT: L 431 ASP cc_start: 0.7774 (m-30) cc_final: 0.7533 (m-30) REVERT: I 59 ASN cc_start: 0.8579 (m-40) cc_final: 0.8093 (p0) REVERT: I 123 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8163 (mtm180) REVERT: I 200 GLU cc_start: 0.7935 (pt0) cc_final: 0.7708 (pt0) REVERT: A 168 GLU cc_start: 0.7484 (mp0) cc_final: 0.7261 (mp0) REVERT: A 183 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 297 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 382 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8816 (p) REVERT: B 278 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8315 (mmm160) REVERT: M 32 TYR cc_start: 0.6938 (m-10) cc_final: 0.6649 (m-80) REVERT: M 34 LYS cc_start: 0.7502 (mmmt) cc_final: 0.6994 (mppt) REVERT: M 35 ILE cc_start: 0.8067 (mp) cc_final: 0.7638 (mt) REVERT: M 37 GLN cc_start: 0.6995 (mp10) cc_final: 0.6681 (mp10) REVERT: M 48 MET cc_start: 0.6092 (ttp) cc_final: 0.5887 (tmm) REVERT: M 95 LYS cc_start: 0.7390 (mttm) cc_final: 0.6832 (mmtt) REVERT: M 96 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5870 (mp) REVERT: M 100 LYS cc_start: 0.5196 (mmtp) cc_final: 0.4674 (ptmt) REVERT: K 18 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.7957 (m110) REVERT: H 26 ASP cc_start: 0.8308 (t0) cc_final: 0.7993 (t0) REVERT: H 299 LYS cc_start: 0.8464 (tttp) cc_final: 0.8241 (tmtt) REVERT: H 349 ASN cc_start: 0.8356 (m-40) cc_final: 0.7792 (t0) REVERT: H 435 TYR cc_start: 0.8763 (m-80) cc_final: 0.8480 (m-10) outliers start: 101 outliers final: 83 residues processed: 518 average time/residue: 0.2375 time to fit residues: 206.4694 Evaluate side-chains 514 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 426 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 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 344 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 254 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 415 GLU 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 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 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 220 THR 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 279 GLU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 306 ASP 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 25 SER 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 241 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 286 LEU 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 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 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 172 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 286 LEU 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: 5.9990 chunk 148 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 154 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 461 optimal weight: 4.9990 chunk 504 optimal weight: 1.9990 chunk 384 optimal weight: 0.9990 chunk 437 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 107 HIS J 216 ASN G 107 HIS ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 331 GLN ** K 88 HIS ** 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 = 0.3552 r_free = 0.3552 target = 0.090151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073898 restraints weight = 90170.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076543 restraints weight = 42456.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078338 restraints weight = 25862.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079553 restraints weight = 18453.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.080367 restraints weight = 14566.826| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43998 Z= 0.116 Angle : 0.534 10.362 59746 Z= 0.270 Chirality : 0.042 0.179 6522 Planarity : 0.004 0.046 7776 Dihedral : 10.446 177.644 5994 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.30 % Allowed : 15.79 % Favored : 81.92 % 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 are not related in a simple way. whole: 1.40 (0.11), residues: 5388 helix: 2.27 (0.10), residues: 2514 sheet: 0.40 (0.18), residues: 768 loop : -0.52 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 278 TYR 0.024 0.001 TYR K 24 PHE 0.012 0.001 PHE I 377 TRP 0.014 0.001 TRP E 21 HIS 0.005 0.001 HIS K 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (43998) covalent geometry : angle 0.53376 / 0.27 (59746) hydrogen bonds : bond 0.04143 / 2.79 ( 2206) hydrogen bonds : angle 4.46069 / 3.26 ( 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 570 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 464 time to evaluate : 1.613 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: 0.8156 (m-30) cc_final: 0.7839 (m-30) REVERT: E 205 ASP cc_start: 0.8126 (t0) cc_final: 0.7843 (t0) REVERT: E 211 ASP cc_start: 0.8281 (t0) cc_final: 0.7888 (t0) REVERT: E 297 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8089 (tm-30) REVERT: F 26 ASP cc_start: 0.8369 (t0) cc_final: 0.8001 (t0) REVERT: F 41 ASP cc_start: 0.7432 (p0) cc_final: 0.7196 (p0) REVERT: F 47 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7872 (mm-30) REVERT: F 137 LEU cc_start: 0.8761 (tt) cc_final: 0.8497 (tp) REVERT: F 138 THR cc_start: 0.8912 (m) cc_final: 0.8584 (p) REVERT: F 174 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8320 (p) REVERT: F 235 MET cc_start: 0.8157 (ttm) cc_final: 0.7759 (mtp) REVERT: F 254 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8605 (mtmt) REVERT: F 332 MET cc_start: 0.8917 (mmp) cc_final: 0.8696 (mmp) REVERT: N 35 ILE cc_start: 0.7903 (mp) cc_final: 0.7524 (mt) REVERT: N 95 LYS cc_start: 0.7653 (mttm) cc_final: 0.6860 (mtmt) REVERT: N 100 LYS cc_start: 0.4803 (mmtp) cc_final: 0.4100 (ptmt) REVERT: J 127 ASP cc_start: 0.8185 (m-30) cc_final: 0.7665 (m-30) REVERT: J 172 TYR cc_start: 0.8607 (t80) cc_final: 0.8294 (t80) REVERT: J 297 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7367 (tm-30) REVERT: J 352 LYS cc_start: 0.8401 (tttm) cc_final: 0.8099 (tppt) REVERT: J 413 MET cc_start: 0.7910 (ttm) cc_final: 0.7640 (ttm) REVERT: J 425 MET cc_start: 0.8600 (tpp) cc_final: 0.8173 (tpp) REVERT: G 47 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7577 (mm-30) REVERT: G 75 MET cc_start: 0.9102 (mmt) cc_final: 0.8697 (mmt) REVERT: G 323 MET cc_start: 0.9077 (pmm) cc_final: 0.7750 (ptp) REVERT: G 393 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 120 ASP cc_start: 0.8177 (m-30) cc_final: 0.7824 (m-30) REVERT: C 168 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: C 205 ASP cc_start: 0.8117 (t0) cc_final: 0.7705 (t0) REVERT: D 69 ASP cc_start: 0.7756 (t0) cc_final: 0.7534 (t0) REVERT: D 127 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7758 (mm-30) REVERT: D 286 LEU cc_start: 0.8333 (pt) cc_final: 0.7862 (pp) REVERT: L 127 ASP cc_start: 0.8133 (m-30) cc_final: 0.7708 (m-30) REVERT: L 306 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8497 (t70) REVERT: L 431 ASP cc_start: 0.7755 (m-30) cc_final: 0.7488 (m-30) REVERT: I 59 ASN cc_start: 0.8560 (m-40) cc_final: 0.8096 (p0) REVERT: I 123 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8166 (mtm180) REVERT: I 200 GLU cc_start: 0.7900 (pt0) cc_final: 0.7696 (pt0) REVERT: A 154 MET cc_start: 0.8815 (mmt) cc_final: 0.8490 (mmm) REVERT: A 183 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 297 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 269 MET cc_start: 0.8340 (mtp) cc_final: 0.8132 (mtm) REVERT: B 278 ARG cc_start: 0.8557 (mmm160) cc_final: 0.8302 (mmm160) REVERT: M 32 TYR cc_start: 0.7032 (m-10) cc_final: 0.6591 (m-80) REVERT: M 34 LYS cc_start: 0.7490 (mmmt) cc_final: 0.6959 (mppt) REVERT: M 35 ILE cc_start: 0.8052 (mp) cc_final: 0.7634 (mt) REVERT: M 37 GLN cc_start: 0.7202 (mp10) cc_final: 0.6854 (mp10) REVERT: M 48 MET cc_start: 0.5964 (ttp) cc_final: 0.5744 (tmm) REVERT: M 95 LYS cc_start: 0.7371 (mttm) cc_final: 0.6820 (mmtt) REVERT: M 96 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5830 (mp) REVERT: M 100 LYS cc_start: 0.5203 (mmtp) cc_final: 0.4733 (ptmt) REVERT: K 302 MET cc_start: 0.7832 (mtm) cc_final: 0.7449 (mpp) REVERT: H 26 ASP cc_start: 0.8293 (t0) cc_final: 0.7935 (t0) REVERT: H 259 MET cc_start: 0.8375 (mmm) cc_final: 0.8107 (mmp) REVERT: H 299 LYS cc_start: 0.8374 (tttp) cc_final: 0.8171 (tmtt) REVERT: H 349 ASN cc_start: 0.8358 (m-40) cc_final: 0.7786 (t0) REVERT: H 435 TYR cc_start: 0.8723 (m-80) cc_final: 0.8505 (m-10) outliers start: 106 outliers final: 84 residues processed: 545 average time/residue: 0.2378 time to fit residues: 218.3034 Evaluate side-chains 523 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 434 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 362 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 242 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 415 GLU 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 223 THR 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 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 220 THR 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 168 GLU 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 340 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 306 ASP Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 286 LEU 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 288 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 241 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 96 LEU 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 23 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 286 LEU 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: 0.0470 chunk 123 optimal weight: 0.9980 chunk 278 optimal weight: 0.9980 chunk 431 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 304 optimal weight: 0.0970 chunk 154 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 378 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 ASN ** I 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** 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** K 18 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS H 436 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074843 restraints weight = 90174.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077513 restraints weight = 42271.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079317 restraints weight = 25608.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080520 restraints weight = 18165.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.081352 restraints weight = 14351.309| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 43998 Z= 0.107 Angle : 0.535 10.379 59746 Z= 0.270 Chirality : 0.041 0.186 6522 Planarity : 0.004 0.046 7776 Dihedral : 10.373 179.680 5993 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.82 % Allowed : 16.57 % Favored : 81.62 % 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 are not related in a simple way. whole: 1.42 (0.12), residues: 5388 helix: 2.23 (0.10), residues: 2550 sheet: 0.47 (0.18), residues: 768 loop : -0.50 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 278 TYR 0.023 0.001 TYR K 24 PHE 0.021 0.001 PHE N 75 TRP 0.015 0.001 TRP C 346 HIS 0.004 0.001 HIS K 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (43998) covalent geometry : angle 0.53521 / 0.27 (59746) hydrogen bonds : bond 0.03910 / 2.63 ( 2206) hydrogen bonds : angle 4.39891 / 3.22 ( 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 559 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 475 time to evaluate : 1.672 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: 0.8176 (m-30) cc_final: 0.7838 (m-30) REVERT: E 127 ASP cc_start: 0.8520 (m-30) cc_final: 0.7831 (t0) REVERT: E 154 MET cc_start: 0.8933 (tpp) cc_final: 0.8626 (tpt) REVERT: E 205 ASP cc_start: 0.8035 (t0) cc_final: 0.7792 (t0) REVERT: E 211 ASP cc_start: 0.8180 (t0) cc_final: 0.7867 (t0) REVERT: E 297 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8069 (tm-30) REVERT: F 26 ASP cc_start: 0.8328 (t0) cc_final: 0.8059 (t0) REVERT: F 41 ASP cc_start: 0.7417 (p0) cc_final: 0.7179 (p0) REVERT: F 47 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7868 (mm-30) REVERT: F 137 LEU cc_start: 0.8703 (tt) cc_final: 0.8433 (tp) REVERT: F 138 THR cc_start: 0.8840 (m) cc_final: 0.8558 (p) REVERT: F 174 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8228 (p) REVERT: F 235 MET cc_start: 0.7958 (ttm) cc_final: 0.7488 (mtp) REVERT: F 254 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8608 (mtmt) REVERT: F 332 MET cc_start: 0.8906 (mmp) cc_final: 0.8688 (mmp) REVERT: N 95 LYS cc_start: 0.7634 (mttm) cc_final: 0.7063 (mmpt) REVERT: J 172 TYR cc_start: 0.8605 (t80) cc_final: 0.8279 (t80) REVERT: J 297 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7360 (tm-30) REVERT: J 313 MET cc_start: 0.8426 (mtm) cc_final: 0.7837 (pmm) REVERT: J 352 LYS cc_start: 0.8369 (tttm) cc_final: 0.8070 (tppt) REVERT: J 413 MET cc_start: 0.7813 (ttm) cc_final: 0.7533 (ttm) REVERT: J 425 MET cc_start: 0.8592 (tpp) cc_final: 0.8184 (tpp) REVERT: G 47 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7578 (mm-30) REVERT: G 75 MET cc_start: 0.9128 (mmt) cc_final: 0.8738 (mmt) REVERT: G 170 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8722 (p) REVERT: G 323 MET cc_start: 0.9082 (pmm) cc_final: 0.7789 (ptp) REVERT: G 393 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7749 (mm-30) REVERT: C 120 ASP cc_start: 0.8179 (m-30) cc_final: 0.7814 (m-30) REVERT: C 205 ASP cc_start: 0.8008 (t0) cc_final: 0.7586 (t0) REVERT: C 212 ILE cc_start: 0.8932 (mt) cc_final: 0.8408 (mm) REVERT: D 69 ASP cc_start: 0.7776 (t0) cc_final: 0.7558 (t0) REVERT: D 127 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7747 (mm-30) REVERT: D 286 LEU cc_start: 0.8294 (pt) cc_final: 0.7818 (pp) REVERT: L 127 ASP cc_start: 0.8088 (m-30) cc_final: 0.7708 (m-30) REVERT: L 145 THR cc_start: 0.8845 (m) cc_final: 0.8627 (p) REVERT: I 59 ASN cc_start: 0.8539 (m-40) cc_final: 0.8081 (p0) REVERT: I 123 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8213 (mtm180) REVERT: I 166 MET cc_start: 0.8345 (tpp) cc_final: 0.8021 (tpt) REVERT: A 183 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 297 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 269 MET cc_start: 0.8343 (mtp) cc_final: 0.8143 (mtm) REVERT: B 278 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8292 (mmm160) REVERT: B 337 ASN cc_start: 0.8739 (m-40) cc_final: 0.8529 (m-40) REVERT: M 32 TYR cc_start: 0.7040 (m-10) cc_final: 0.6602 (m-80) REVERT: M 34 LYS cc_start: 0.7487 (mmmt) cc_final: 0.6966 (mppt) REVERT: M 35 ILE cc_start: 0.8064 (mp) cc_final: 0.7637 (mt) REVERT: M 37 GLN cc_start: 0.7212 (mp10) cc_final: 0.6856 (mp10) REVERT: M 48 MET cc_start: 0.5919 (ttp) cc_final: 0.5664 (tmm) REVERT: M 95 LYS cc_start: 0.7371 (mttm) cc_final: 0.6821 (mmtt) REVERT: M 96 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5868 (mp) REVERT: M 100 LYS cc_start: 0.5270 (mmtp) cc_final: 0.4786 (ptmt) REVERT: H 26 ASP cc_start: 0.8297 (t0) cc_final: 0.7936 (t0) REVERT: H 202 TYR cc_start: 0.9023 (m-80) cc_final: 0.8110 (m-80) REVERT: H 259 MET cc_start: 0.8531 (mmm) cc_final: 0.8156 (mmp) REVERT: H 349 ASN cc_start: 0.8361 (m-40) cc_final: 0.7778 (t0) outliers start: 84 outliers final: 72 residues processed: 539 average time/residue: 0.2400 time to fit residues: 217.1887 Evaluate side-chains 513 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 437 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 344 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 48 MET Chi-restraints excluded: chain J residue 130 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 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 145 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU 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 269 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 190 THR 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 141 LEU Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 286 LEU 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 288 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 286 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain M residue 56 VAL 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 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 286 LEU 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 222 optimal weight: 0.5980 chunk 449 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 230 optimal weight: 0.0010 chunk 476 optimal weight: 0.9980 chunk 331 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 chunk 443 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 469 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 258 ASN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 ASN I 436 GLN ** 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** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.091808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075616 restraints weight = 90452.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078286 restraints weight = 42313.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080108 restraints weight = 25620.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081323 restraints weight = 18141.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082154 restraints weight = 14275.046| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 43998 Z= 0.106 Angle : 0.537 10.090 59746 Z= 0.271 Chirality : 0.041 0.162 6522 Planarity : 0.004 0.045 7776 Dihedral : 10.290 177.589 5991 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.84 % Allowed : 16.67 % Favored : 81.49 % 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 are not related in a simple way. whole: 1.45 (0.12), residues: 5388 helix: 2.25 (0.10), residues: 2546 sheet: 0.50 (0.19), residues: 768 loop : -0.49 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 278 TYR 0.024 0.001 TYR L 24 PHE 0.016 0.001 PHE N 75 TRP 0.015 0.001 TRP C 346 HIS 0.004 0.001 HIS K 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (43998) covalent geometry : angle 0.53704 / 0.27 (59746) hydrogen bonds : bond 0.03785 / 2.55 ( 2206) hydrogen bonds : angle 4.36400 / 3.19 ( 6408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7486.02 seconds wall clock time: 130 minutes 46.97 seconds (7846.97 seconds total)