Starting phenix.real_space_refine on Fri Mar 6 02:49:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4i_31712/03_2026/7v4i_31712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4i_31712/03_2026/7v4i_31712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v4i_31712/03_2026/7v4i_31712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4i_31712/03_2026/7v4i_31712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v4i_31712/03_2026/7v4i_31712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4i_31712/03_2026/7v4i_31712.map" } resolution = 3.3 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17560 2.51 5 N 4740 2.21 5 O 5260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27680 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "B" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "C" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "D" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "E" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "F" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "G" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "H" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "I" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Time building chain proxies: 6.29, per 1000 atoms: 0.23 Number of scatterers: 27680 At special positions: 0 Unit cell: (138.514, 138.514, 109.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5260 8.00 N 4740 7.00 C 17560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 30 sheets defined 33.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'J' and resid 11 through 15 removed outlier: 3.898A pdb=" N GLU J 14 " --> pdb=" O ASN J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 57 through 61 Processing helix chain 'J' and resid 107 through 115 Processing helix chain 'J' and resid 116 through 123 removed outlier: 3.724A pdb=" N GLU J 123 " --> pdb=" O VAL J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 183 removed outlier: 4.045A pdb=" N VAL J 172 " --> pdb=" O GLY J 168 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY J 183 " --> pdb=" O CYS J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 228 Processing helix chain 'J' and resid 262 through 276 removed outlier: 4.205A pdb=" N LYS J 267 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS J 268 " --> pdb=" O GLU J 264 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS J 276 " --> pdb=" O LYS J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 Processing helix chain 'J' and resid 287 through 292 removed outlier: 3.891A pdb=" N ARG J 291 " --> pdb=" O GLY J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 325 Processing helix chain 'J' and resid 339 through 353 Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.688A pdb=" N CYS A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4 through 9' Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.695A pdb=" N LEU A 50 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 168 through 183 removed outlier: 4.181A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 229 Processing helix chain 'A' and resid 262 through 276 removed outlier: 4.077A pdb=" N LYS A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.614A pdb=" N ARG A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 325 removed outlier: 3.626A pdb=" N GLU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.983A pdb=" N VAL B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 228 removed outlier: 3.894A pdb=" N GLY B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 261 through 276 removed outlier: 4.292A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.540A pdb=" N HIS B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.566A pdb=" N ARG B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.588A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 183 " --> pdb=" O CYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 228 removed outlier: 3.976A pdb=" N ASP C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 262 through 276 removed outlier: 4.138A pdb=" N LYS C 276 " --> pdb=" O LYS C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.096A pdb=" N ARG C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 339 through 353 removed outlier: 3.966A pdb=" N ALA C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 122 Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.967A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 183 " --> pdb=" O CYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.281A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 276 removed outlier: 4.070A pdb=" N LYS D 276 " --> pdb=" O LYS D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 287 through 292 removed outlier: 4.136A pdb=" N ARG D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 4 through 9 removed outlier: 3.654A pdb=" N CYS E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 9' Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.728A pdb=" N LEU E 50 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.525A pdb=" N GLY E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 57 through 61' Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 116 through 123 Processing helix chain 'E' and resid 169 through 183 Processing helix chain 'E' and resid 208 through 229 Processing helix chain 'E' and resid 262 through 276 removed outlier: 4.094A pdb=" N LYS E 276 " --> pdb=" O LYS E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 284 removed outlier: 3.829A pdb=" N HIS E 280 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.644A pdb=" N ARG E 290 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.605A pdb=" N GLU E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 4 through 9 removed outlier: 3.668A pdb=" N ASN F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 107 through 115 Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 168 through 183 removed outlier: 3.715A pdb=" N VAL F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 229 removed outlier: 4.196A pdb=" N ASP F 212 " --> pdb=" O ILE F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 276 removed outlier: 4.393A pdb=" N VAL F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 339 through 353 Processing helix chain 'G' and resid 4 through 9 removed outlier: 3.723A pdb=" N ASN G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 removed outlier: 3.600A pdb=" N LEU G 50 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 115 Processing helix chain 'G' and resid 116 through 123 Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.706A pdb=" N VAL G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 228 Processing helix chain 'G' and resid 262 through 276 removed outlier: 3.647A pdb=" N LYS G 276 " --> pdb=" O LYS G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 283 removed outlier: 3.521A pdb=" N HIS G 280 " --> pdb=" O LYS G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 318 through 325 Processing helix chain 'G' and resid 339 through 353 Processing helix chain 'H' and resid 4 through 9 removed outlier: 3.757A pdb=" N ASN H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.951A pdb=" N LEU H 50 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 115 Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.729A pdb=" N VAL H 172 " --> pdb=" O GLY H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 229 Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 262 through 276 removed outlier: 3.548A pdb=" N LYS H 276 " --> pdb=" O LYS H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 283 Processing helix chain 'H' and resid 287 through 292 removed outlier: 4.094A pdb=" N ARG H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 325 Processing helix chain 'H' and resid 339 through 353 Processing helix chain 'I' and resid 46 through 50 Processing helix chain 'I' and resid 107 through 115 Processing helix chain 'I' and resid 116 through 123 Processing helix chain 'I' and resid 168 through 183 removed outlier: 3.954A pdb=" N VAL I 172 " --> pdb=" O GLY I 168 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY I 183 " --> pdb=" O CYS I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 229 removed outlier: 4.407A pdb=" N GLY I 211 " --> pdb=" O GLY I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 259 Processing helix chain 'I' and resid 262 through 275 removed outlier: 4.257A pdb=" N LYS I 267 " --> pdb=" O PHE I 263 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS I 268 " --> pdb=" O GLU I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 283 Processing helix chain 'I' and resid 287 through 291 removed outlier: 3.564A pdb=" N ARG I 290 " --> pdb=" O GLY I 287 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG I 291 " --> pdb=" O ASN I 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 287 through 291' Processing helix chain 'I' and resid 318 through 325 Processing helix chain 'I' and resid 339 through 353 Processing sheet with id=AA1, first strand: chain 'J' and resid 53 through 56 removed outlier: 4.169A pdb=" N TRP J 53 " --> pdb=" O LEU J 72 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET J 91 " --> pdb=" O GLN J 75 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE J 77 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU J 89 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE J 20 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL J 90 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU J 22 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N CYS J 92 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE J 24 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA J 94 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE J 26 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N SER J 35 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY D 191 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER D 187 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN D 201 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLY D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN D 197 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.616A pdb=" N THR J 133 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR J 252 " --> pdb=" O PHE J 329 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE J 329 " --> pdb=" O TYR J 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.616A pdb=" N THR J 133 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER J 205 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE J 128 " --> pdb=" O GLY J 203 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY J 203 " --> pdb=" O ILE J 128 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN J 130 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN J 201 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR J 132 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU J 199 " --> pdb=" O TYR J 132 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU J 134 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN J 197 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLN J 197 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU J 199 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN J 201 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N SER J 187 " --> pdb=" O THR I 39 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY J 191 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N SER I 35 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE I 20 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL I 90 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU I 22 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS I 92 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE I 24 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA I 94 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ILE I 26 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA I 76 " --> pdb=" O MET I 91 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP I 93 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR I 95 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU I 72 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TRP I 53 " --> pdb=" O LEU I 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.611A pdb=" N GLU A 22 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS A 92 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 24 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A 94 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE A 26 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 76 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 93 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 95 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU A 72 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 53 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.649A pdb=" N GLN A 201 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 189 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU A 199 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 132 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 128 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.573A pdb=" N SER A 205 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 249 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 252 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 329 " --> pdb=" O TYR A 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 removed outlier: 4.015A pdb=" N TRP B 53 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET B 91 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 77 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 89 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE B 20 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL B 90 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS B 92 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE B 24 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 94 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE B 26 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP B 25 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N SER B 35 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY I 191 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER I 187 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN I 201 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU I 199 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN I 197 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN I 130 " --> pdb=" O PHE I 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.519A pdb=" N TYR B 252 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 329 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 307 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 233 removed outlier: 5.672A pdb=" N TYR B 126 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 128 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 130 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN B 197 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLY B 191 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU B 199 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE B 189 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN B 201 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER B 187 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY B 191 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N SER C 35 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE C 20 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL C 90 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU C 22 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N CYS C 92 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE C 24 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA C 94 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ILE C 26 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 76 " --> pdb=" O MET C 91 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP C 93 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR C 95 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU C 72 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP C 53 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.615A pdb=" N TYR C 252 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE C 329 " --> pdb=" O TYR C 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 231 through 233 removed outlier: 6.118A pdb=" N TYR C 126 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 128 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 130 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 200 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 187 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY C 191 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N SER D 35 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE D 20 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL D 90 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU D 22 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS D 92 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 24 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA D 94 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE D 26 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU D 89 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE D 77 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N MET D 91 " --> pdb=" O GLN D 75 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP D 53 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 206 removed outlier: 3.617A pdb=" N TYR D 252 " --> pdb=" O PHE D 329 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 329 " --> pdb=" O TYR D 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.641A pdb=" N ASP E 93 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 76 " --> pdb=" O MET E 91 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE E 26 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG E 38 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N SER E 35 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY F 191 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY F 188 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR F 126 " --> pdb=" O SER F 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.641A pdb=" N ASP E 93 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 76 " --> pdb=" O MET E 91 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE E 26 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG E 38 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N SER E 35 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY F 191 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY F 188 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS F 249 " --> pdb=" O GLU F 129 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE F 329 " --> pdb=" O TYR F 252 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY F 307 " --> pdb=" O VAL F 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 186 through 191 removed outlier: 4.633A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 128 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR E 126 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER E 205 " --> pdb=" O TYR E 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 186 through 191 removed outlier: 4.633A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 128 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS E 249 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR E 252 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 329 " --> pdb=" O TYR E 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 133 through 135 Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 36 removed outlier: 6.263A pdb=" N GLU F 22 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS F 92 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE F 24 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA F 94 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ILE F 26 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 76 " --> pdb=" O MET F 91 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP F 93 " --> pdb=" O PRO F 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 133 through 135 removed outlier: 3.505A pdb=" N THR F 133 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 36 removed outlier: 6.683A pdb=" N GLU G 22 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS G 92 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE G 24 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA G 94 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE G 26 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA G 76 " --> pdb=" O MET G 91 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP G 93 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 186 through 189 removed outlier: 6.663A pdb=" N GLN G 201 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE G 128 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER G 205 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 186 through 189 removed outlier: 6.663A pdb=" N GLN G 201 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE G 128 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE G 329 " --> pdb=" O TYR G 252 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY G 307 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL G 317 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 133 through 135 removed outlier: 3.622A pdb=" N THR G 133 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 233 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 33 through 36 removed outlier: 3.501A pdb=" N TYR H 23 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU H 22 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N CYS H 92 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE H 24 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA H 94 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE H 26 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR H 96 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET H 91 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA H 76 " --> pdb=" O MET H 91 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP H 93 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR H 95 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU H 72 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP H 53 " --> pdb=" O LEU H 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 33 through 36 removed outlier: 3.501A pdb=" N TYR H 23 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU H 22 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N CYS H 92 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE H 24 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA H 94 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE H 26 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR H 96 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 186 through 191 removed outlier: 4.371A pdb=" N GLY H 188 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN H 130 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 128 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR H 126 " --> pdb=" O SER H 205 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 205 " --> pdb=" O TYR H 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 186 through 191 removed outlier: 4.371A pdb=" N GLY H 188 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN H 130 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 128 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE H 329 " --> pdb=" O TYR H 252 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLY H 307 " --> pdb=" O VAL H 317 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 133 through 135 Processing sheet with id=AD2, first strand: chain 'I' and resid 125 through 127 Processing sheet with id=AD3, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.535A pdb=" N GLY I 307 " --> pdb=" O ILE I 315 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 2961 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: 5.04 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9083 1.34 - 1.46: 5169 1.46 - 1.58: 13968 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 28420 Sorted by residual: bond pdb=" N ARG A 84 " pdb=" CA ARG A 84 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.39e+00 bond pdb=" N VAL C 206 " pdb=" CA VAL C 206 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.23e-02 6.61e+03 1.26e+00 bond pdb=" N ARG J 84 " pdb=" CA ARG J 84 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" C ARG B 333 " pdb=" N PRO B 334 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.33e-02 5.65e+03 9.96e-01 bond pdb=" CA ARG B 333 " pdb=" C ARG B 333 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.81e-01 ... (remaining 28415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 37746 1.70 - 3.41: 721 3.41 - 5.11: 94 5.11 - 6.81: 22 6.81 - 8.52: 7 Bond angle restraints: 38590 Sorted by residual: angle pdb=" C LYS F 326 " pdb=" CA LYS F 326 " pdb=" CB LYS F 326 " ideal model delta sigma weight residual 116.54 109.51 7.03 1.15e+00 7.56e-01 3.73e+01 angle pdb=" C ARG F 84 " pdb=" CA ARG F 84 " pdb=" CB ARG F 84 " ideal model delta sigma weight residual 115.79 110.14 5.65 1.19e+00 7.06e-01 2.25e+01 angle pdb=" C ARG B 84 " pdb=" CA ARG B 84 " pdb=" CB ARG B 84 " ideal model delta sigma weight residual 115.79 110.21 5.58 1.19e+00 7.06e-01 2.20e+01 angle pdb=" C ARG C 84 " pdb=" CA ARG C 84 " pdb=" CB ARG C 84 " ideal model delta sigma weight residual 115.79 110.60 5.19 1.19e+00 7.06e-01 1.90e+01 angle pdb=" CA LYS F 326 " pdb=" C LYS F 326 " pdb=" N GLY F 327 " ideal model delta sigma weight residual 119.52 116.52 3.00 7.90e-01 1.60e+00 1.44e+01 ... (remaining 38585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 15104 18.01 - 36.01: 1380 36.01 - 54.02: 210 54.02 - 72.02: 48 72.02 - 90.03: 28 Dihedral angle restraints: 16770 sinusoidal: 6730 harmonic: 10040 Sorted by residual: dihedral pdb=" CA GLU F 192 " pdb=" C GLU F 192 " pdb=" N VAL F 193 " pdb=" CA VAL F 193 " ideal model delta harmonic sigma weight residual -180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS F 140 " pdb=" C LYS F 140 " pdb=" N TRP F 141 " pdb=" CA TRP F 141 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA GLU E 192 " pdb=" C GLU E 192 " pdb=" N VAL E 193 " pdb=" CA VAL E 193 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 16767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2742 0.041 - 0.082: 893 0.082 - 0.123: 333 0.123 - 0.164: 21 0.164 - 0.204: 1 Chirality restraints: 3990 Sorted by residual: chirality pdb=" CA ARG B 333 " pdb=" N ARG B 333 " pdb=" C ARG B 333 " pdb=" CB ARG B 333 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE J 102 " pdb=" N ILE J 102 " pdb=" C ILE J 102 " pdb=" CB ILE J 102 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE C 102 " pdb=" N ILE C 102 " pdb=" C ILE C 102 " pdb=" CB ILE C 102 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 3987 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 354 " -0.029 2.00e-02 2.50e+03 2.69e-02 1.81e+01 pdb=" CG TRP F 354 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP F 354 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP F 354 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 354 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 354 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 354 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 354 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 354 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP F 354 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 333 " -0.053 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 334 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 100 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.40e+00 pdb=" N PRO F 101 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO F 101 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 101 " 0.042 5.00e-02 4.00e+02 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 337 2.64 - 3.21: 25040 3.21 - 3.77: 42661 3.77 - 4.34: 57223 4.34 - 4.90: 96588 Nonbonded interactions: 221849 Sorted by model distance: nonbonded pdb=" OG1 THR F 39 " pdb=" OH TYR G 176 " model vdw 2.079 3.040 nonbonded pdb=" OH TYR C 176 " pdb=" OG1 THR D 39 " model vdw 2.102 3.040 nonbonded pdb=" OG SER E 233 " pdb=" OD1 ASP E 235 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR A 176 " pdb=" OG1 THR G 39 " model vdw 2.144 3.040 nonbonded pdb=" OH TYR E 176 " pdb=" OG1 THR H 39 " model vdw 2.150 3.040 ... (remaining 221844 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.740 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 24.500 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.003 0.036 28420 Z= 0.124 Angle : 0.585 8.515 38590 Z= 0.308 Chirality : 0.044 0.204 3990 Planarity : 0.006 0.079 5070 Dihedral : 14.199 90.031 10450 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3540 helix: 1.09 (0.17), residues: 1000 sheet: -1.14 (0.18), residues: 810 loop : -1.70 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 278 TYR 0.025 0.001 TYR I 176 PHE 0.007 0.001 PHE G 329 TRP 0.072 0.002 TRP F 354 HIS 0.018 0.001 HIS I 175 Details of bonding type rmsd covalent geometry : bond 0.00280 (28420) covalent geometry : angle 0.58497 (38590) hydrogen bonds : bond 0.20953 ( 1009) hydrogen bonds : angle 7.29343 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: J 16 THR cc_start: 0.8168 (t) cc_final: 0.7781 (p) REVERT: C 221 LEU cc_start: 0.7483 (tt) cc_final: 0.7238 (tt) REVERT: D 257 MET cc_start: 0.8381 (mtp) cc_final: 0.8150 (mtp) REVERT: F 31 MET cc_start: 0.6997 (tpp) cc_final: 0.6713 (tpt) REVERT: F 326 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7447 (mmmt) REVERT: G 31 MET cc_start: 0.7144 (tpp) cc_final: 0.6675 (tpt) REVERT: H 216 MET cc_start: 0.7309 (mmm) cc_final: 0.7100 (mmm) REVERT: I 91 MET cc_start: 0.5793 (tpt) cc_final: 0.5559 (tpt) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1695 time to fit residues: 98.0526 Evaluate side-chains 268 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.221934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.165365 restraints weight = 36185.927| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 4.46 r_work: 0.4007 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28420 Z= 0.134 Angle : 0.580 9.005 38590 Z= 0.302 Chirality : 0.045 0.171 3990 Planarity : 0.005 0.064 5070 Dihedral : 4.238 19.423 3900 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.48 % Allowed : 8.79 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3540 helix: 1.55 (0.17), residues: 880 sheet: -1.03 (0.18), residues: 850 loop : -1.57 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 107 TYR 0.019 0.001 TYR I 252 PHE 0.014 0.001 PHE F 329 TRP 0.053 0.001 TRP F 354 HIS 0.012 0.001 HIS J 175 Details of bonding type rmsd covalent geometry : bond 0.00314 (28420) covalent geometry : angle 0.58035 (38590) hydrogen bonds : bond 0.04382 ( 1009) hydrogen bonds : angle 5.35851 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 318 time to evaluate : 0.762 Fit side-chains REVERT: J 49 LYS cc_start: 0.8995 (mttt) cc_final: 0.8565 (mttp) REVERT: J 255 LYS cc_start: 0.7494 (tptt) cc_final: 0.7077 (tptp) REVERT: A 31 MET cc_start: 0.7544 (tpp) cc_final: 0.7204 (tpt) REVERT: A 257 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.5929 (mtm) REVERT: A 306 TRP cc_start: 0.7704 (p-90) cc_final: 0.7385 (p-90) REVERT: B 125 TRP cc_start: 0.5684 (m-10) cc_final: 0.5479 (m-10) REVERT: B 145 TRP cc_start: 0.8152 (t-100) cc_final: 0.7474 (t-100) REVERT: B 310 ASN cc_start: 0.6278 (t0) cc_final: 0.6075 (t0) REVERT: C 222 GLU cc_start: 0.8145 (tt0) cc_final: 0.7841 (pt0) REVERT: C 316 ARG cc_start: 0.6926 (ttp80) cc_final: 0.6268 (tmm-80) REVERT: D 213 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.5235 (mp-120) REVERT: E 31 MET cc_start: 0.7635 (tpp) cc_final: 0.7253 (tpt) REVERT: F 235 ASP cc_start: 0.8087 (p0) cc_final: 0.7667 (p0) REVERT: H 216 MET cc_start: 0.7826 (mmm) cc_final: 0.7535 (mmm) REVERT: I 91 MET cc_start: 0.5797 (tpt) cc_final: 0.5423 (tpt) REVERT: I 129 GLU cc_start: 0.5928 (mt-10) cc_final: 0.5387 (mt-10) REVERT: I 213 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5089 (mp-120) outliers start: 14 outliers final: 7 residues processed: 324 average time/residue: 0.1821 time to fit residues: 93.5550 Evaluate side-chains 279 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 269 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 346 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 244 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 14 optimal weight: 0.0050 chunk 334 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 overall best weight: 0.7534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 41 ASN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN D 197 GLN E 62 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.244091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.175469 restraints weight = 36922.346| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 3.17 r_work: 0.4136 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28420 Z= 0.102 Angle : 0.535 7.974 38590 Z= 0.276 Chirality : 0.044 0.167 3990 Planarity : 0.005 0.067 5070 Dihedral : 3.955 17.571 3900 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.87 % Allowed : 11.18 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3540 helix: 1.29 (0.17), residues: 950 sheet: -0.86 (0.18), residues: 850 loop : -1.56 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 278 TYR 0.030 0.001 TYR C 176 PHE 0.014 0.001 PHE H 234 TRP 0.064 0.001 TRP F 354 HIS 0.010 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00236 (28420) covalent geometry : angle 0.53510 (38590) hydrogen bonds : bond 0.03630 ( 1009) hydrogen bonds : angle 4.91369 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 306 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.6071 (mtm) REVERT: A 306 TRP cc_start: 0.7666 (p-90) cc_final: 0.7311 (p-90) REVERT: B 145 TRP cc_start: 0.8197 (t-100) cc_final: 0.7397 (t-100) REVERT: B 310 ASN cc_start: 0.6392 (t0) cc_final: 0.6168 (t0) REVERT: C 125 TRP cc_start: 0.5700 (m-10) cc_final: 0.5462 (m-10) REVERT: C 175 HIS cc_start: 0.7873 (t-90) cc_final: 0.7660 (t70) REVERT: D 107 ARG cc_start: 0.5570 (ttt180) cc_final: 0.5327 (ttt180) REVERT: D 213 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.5159 (mp-120) REVERT: F 235 ASP cc_start: 0.7820 (p0) cc_final: 0.7541 (p0) REVERT: G 31 MET cc_start: 0.7240 (tpp) cc_final: 0.6820 (tpt) REVERT: G 62 GLN cc_start: 0.6776 (pt0) cc_final: 0.6567 (pt0) REVERT: H 1 MET cc_start: 0.2887 (pmm) cc_final: 0.1647 (ptt) REVERT: H 123 GLU cc_start: 0.8134 (mp0) cc_final: 0.7442 (mp0) REVERT: H 257 MET cc_start: 0.6482 (mtt) cc_final: 0.6075 (mtt) REVERT: I 91 MET cc_start: 0.5951 (tpt) cc_final: 0.5602 (tpt) REVERT: I 108 PHE cc_start: 0.7701 (t80) cc_final: 0.7457 (t80) REVERT: I 213 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.5340 (mp-120) outliers start: 25 outliers final: 12 residues processed: 323 average time/residue: 0.1799 time to fit residues: 92.4435 Evaluate side-chains 293 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 213 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 169 optimal weight: 0.4980 chunk 244 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 287 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 278 optimal weight: 0.2980 chunk 96 optimal weight: 40.0000 chunk 183 optimal weight: 0.0770 chunk 311 optimal weight: 9.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 62 GLN E 62 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.245098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.176471 restraints weight = 36573.513| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 3.17 r_work: 0.4141 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28420 Z= 0.093 Angle : 0.517 7.673 38590 Z= 0.265 Chirality : 0.043 0.156 3990 Planarity : 0.005 0.065 5070 Dihedral : 3.754 17.088 3900 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.00 % Allowed : 12.60 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3540 helix: 1.33 (0.17), residues: 950 sheet: -0.78 (0.18), residues: 850 loop : -1.49 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 278 TYR 0.021 0.001 TYR F 252 PHE 0.011 0.001 PHE F 329 TRP 0.060 0.001 TRP F 354 HIS 0.011 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00214 (28420) covalent geometry : angle 0.51734 (38590) hydrogen bonds : bond 0.03209 ( 1009) hydrogen bonds : angle 4.70267 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 317 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 138 GLU cc_start: 0.8237 (pt0) cc_final: 0.7978 (mt-10) REVERT: A 306 TRP cc_start: 0.7641 (p-90) cc_final: 0.7276 (p-90) REVERT: B 145 TRP cc_start: 0.8187 (t-100) cc_final: 0.7286 (m-90) REVERT: B 310 ASN cc_start: 0.6365 (t0) cc_final: 0.6136 (t0) REVERT: C 125 TRP cc_start: 0.5721 (m-10) cc_final: 0.5504 (m-10) REVERT: C 222 GLU cc_start: 0.7908 (tt0) cc_final: 0.7440 (tt0) REVERT: D 107 ARG cc_start: 0.5705 (OUTLIER) cc_final: 0.4761 (ttt180) REVERT: D 213 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.5129 (mp-120) REVERT: E 31 MET cc_start: 0.7518 (tpp) cc_final: 0.6993 (tpt) REVERT: E 235 ASP cc_start: 0.7722 (p0) cc_final: 0.7368 (p0) REVERT: G 31 MET cc_start: 0.7317 (tpp) cc_final: 0.6977 (tpt) REVERT: G 216 MET cc_start: 0.7655 (mmm) cc_final: 0.7414 (mmm) REVERT: H 1 MET cc_start: 0.2801 (pmm) cc_final: 0.1706 (ptt) REVERT: H 123 GLU cc_start: 0.8089 (mp0) cc_final: 0.7391 (mp0) REVERT: H 257 MET cc_start: 0.6294 (mtt) cc_final: 0.5980 (mtt) REVERT: H 286 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6645 (pm20) REVERT: I 91 MET cc_start: 0.5920 (tpt) cc_final: 0.5543 (tpt) REVERT: I 213 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.5381 (mp-120) outliers start: 29 outliers final: 18 residues processed: 334 average time/residue: 0.1831 time to fit residues: 96.1887 Evaluate side-chains 307 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 286 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain I residue 213 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 172 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 4 optimal weight: 0.0970 chunk 34 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 314 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 175 HIS ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.243879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.175847 restraints weight = 36293.152| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 3.06 r_work: 0.4133 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28420 Z= 0.100 Angle : 0.524 7.888 38590 Z= 0.267 Chirality : 0.043 0.163 3990 Planarity : 0.005 0.064 5070 Dihedral : 3.740 17.121 3900 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.70 % Allowed : 13.22 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3540 helix: 1.32 (0.17), residues: 950 sheet: -0.73 (0.18), residues: 850 loop : -1.47 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 278 TYR 0.032 0.001 TYR H 252 PHE 0.011 0.001 PHE F 329 TRP 0.051 0.001 TRP F 354 HIS 0.011 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00235 (28420) covalent geometry : angle 0.52409 (38590) hydrogen bonds : bond 0.03251 ( 1009) hydrogen bonds : angle 4.62040 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 125 TRP cc_start: 0.5608 (m-10) cc_final: 0.5319 (m-10) REVERT: J 138 GLU cc_start: 0.8204 (pt0) cc_final: 0.7984 (mt-10) REVERT: A 31 MET cc_start: 0.7324 (tpp) cc_final: 0.7087 (tpt) REVERT: A 306 TRP cc_start: 0.7673 (p-90) cc_final: 0.7294 (p-90) REVERT: B 123 GLU cc_start: 0.8263 (mp0) cc_final: 0.8059 (mp0) REVERT: B 145 TRP cc_start: 0.8214 (t-100) cc_final: 0.7326 (m-90) REVERT: B 310 ASN cc_start: 0.6330 (t0) cc_final: 0.6101 (t0) REVERT: C 125 TRP cc_start: 0.5786 (m-10) cc_final: 0.5534 (m-10) REVERT: C 222 GLU cc_start: 0.7801 (tt0) cc_final: 0.7322 (tt0) REVERT: D 107 ARG cc_start: 0.5322 (OUTLIER) cc_final: 0.5077 (ttt180) REVERT: D 213 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.5253 (mp-120) REVERT: E 31 MET cc_start: 0.7485 (tpp) cc_final: 0.7057 (tpt) REVERT: E 257 MET cc_start: 0.5559 (mtp) cc_final: 0.4403 (mtp) REVERT: F 31 MET cc_start: 0.7184 (tpp) cc_final: 0.6814 (tpt) REVERT: G 31 MET cc_start: 0.7278 (tpp) cc_final: 0.6994 (tpt) REVERT: G 284 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: H 1 MET cc_start: 0.2916 (pmm) cc_final: 0.1834 (ptt) REVERT: H 123 GLU cc_start: 0.8157 (mp0) cc_final: 0.7469 (mp0) REVERT: H 286 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6697 (pm20) REVERT: I 91 MET cc_start: 0.5887 (tpt) cc_final: 0.5562 (tpt) REVERT: I 123 GLU cc_start: 0.8503 (mp0) cc_final: 0.8185 (mp0) REVERT: I 213 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.5430 (mp-120) outliers start: 49 outliers final: 29 residues processed: 342 average time/residue: 0.1714 time to fit residues: 92.7460 Evaluate side-chains 317 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 284 TYR Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 52 GLN Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 346 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 126 optimal weight: 6.9990 chunk 292 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 275 optimal weight: 9.9990 chunk 321 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 175 HIS C 197 GLN D 197 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.240784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.166604 restraints weight = 36841.762| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 3.08 r_work: 0.4051 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28420 Z= 0.185 Angle : 0.605 9.646 38590 Z= 0.310 Chirality : 0.046 0.162 3990 Planarity : 0.005 0.063 5070 Dihedral : 4.278 21.813 3900 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.94 % Allowed : 13.56 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3540 helix: 1.19 (0.17), residues: 950 sheet: -0.84 (0.18), residues: 850 loop : -1.58 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 278 TYR 0.019 0.002 TYR J 284 PHE 0.018 0.002 PHE F 329 TRP 0.050 0.002 TRP F 354 HIS 0.016 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00449 (28420) covalent geometry : angle 0.60485 (38590) hydrogen bonds : bond 0.04129 ( 1009) hydrogen bonds : angle 4.87069 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 125 TRP cc_start: 0.5649 (m-10) cc_final: 0.5315 (m-10) REVERT: J 352 ILE cc_start: 0.8010 (tp) cc_final: 0.7777 (tp) REVERT: A 286 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6973 (pm20) REVERT: B 123 GLU cc_start: 0.8251 (mp0) cc_final: 0.7808 (mp0) REVERT: C 41 ASN cc_start: 0.8604 (m-40) cc_final: 0.8223 (p0) REVERT: C 125 TRP cc_start: 0.5807 (m-10) cc_final: 0.5587 (m-10) REVERT: C 222 GLU cc_start: 0.7876 (tt0) cc_final: 0.7537 (tt0) REVERT: D 107 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.5165 (ttt180) REVERT: D 123 GLU cc_start: 0.8675 (mp0) cc_final: 0.8432 (mp0) REVERT: D 129 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6490 (pt0) REVERT: D 213 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.5560 (mp-120) REVERT: D 316 ARG cc_start: 0.7412 (tmm-80) cc_final: 0.7170 (tmm-80) REVERT: E 319 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7036 (mtm-85) REVERT: H 1 MET cc_start: 0.2980 (pmm) cc_final: 0.1911 (ptt) REVERT: H 31 MET cc_start: 0.7376 (tpp) cc_final: 0.6686 (tpt) REVERT: H 286 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6900 (pm20) REVERT: H 289 GLU cc_start: 0.7737 (pm20) cc_final: 0.7456 (mp0) REVERT: I 41 ASN cc_start: 0.8565 (m-40) cc_final: 0.8347 (p0) REVERT: I 91 MET cc_start: 0.5859 (tpt) cc_final: 0.5592 (tpt) REVERT: I 213 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.5282 (mp-120) outliers start: 56 outliers final: 38 residues processed: 341 average time/residue: 0.1854 time to fit residues: 99.5375 Evaluate side-chains 317 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 346 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 182 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 335 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 259 optimal weight: 0.4980 chunk 140 optimal weight: 0.4980 chunk 327 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 332 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.239208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.168703 restraints weight = 36652.773| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.15 r_work: 0.4057 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28420 Z= 0.136 Angle : 0.576 9.302 38590 Z= 0.292 Chirality : 0.045 0.162 3990 Planarity : 0.005 0.065 5070 Dihedral : 4.164 19.799 3900 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.76 % Allowed : 14.50 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3540 helix: 1.19 (0.17), residues: 950 sheet: -0.87 (0.18), residues: 850 loop : -1.56 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 278 TYR 0.029 0.001 TYR E 252 PHE 0.015 0.001 PHE F 329 TRP 0.045 0.001 TRP F 354 HIS 0.015 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00329 (28420) covalent geometry : angle 0.57580 (38590) hydrogen bonds : bond 0.03710 ( 1009) hydrogen bonds : angle 4.76936 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 125 TRP cc_start: 0.5583 (m-10) cc_final: 0.5264 (m-10) REVERT: J 352 ILE cc_start: 0.7938 (tp) cc_final: 0.7722 (tp) REVERT: A 31 MET cc_start: 0.7356 (tpp) cc_final: 0.6921 (tpt) REVERT: A 286 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6868 (pm20) REVERT: A 319 ARG cc_start: 0.7333 (mtp85) cc_final: 0.7085 (mtp85) REVERT: B 123 GLU cc_start: 0.8248 (mp0) cc_final: 0.7836 (mp0) REVERT: C 41 ASN cc_start: 0.8670 (m-40) cc_final: 0.8219 (p0) REVERT: C 125 TRP cc_start: 0.5699 (m-10) cc_final: 0.5433 (m-10) REVERT: C 222 GLU cc_start: 0.7947 (tt0) cc_final: 0.7585 (tt0) REVERT: D 107 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.5101 (ttt180) REVERT: D 129 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6362 (pt0) REVERT: D 213 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.5164 (mp-120) REVERT: E 31 MET cc_start: 0.7440 (tpp) cc_final: 0.6910 (tpt) REVERT: F 31 MET cc_start: 0.7302 (tpp) cc_final: 0.6775 (tpt) REVERT: F 131 GLU cc_start: 0.8008 (pm20) cc_final: 0.7509 (pm20) REVERT: F 317 VAL cc_start: 0.7904 (t) cc_final: 0.7615 (p) REVERT: G 31 MET cc_start: 0.7319 (tpp) cc_final: 0.6827 (tpt) REVERT: G 257 MET cc_start: 0.5427 (OUTLIER) cc_final: 0.4759 (mtm) REVERT: H 1 MET cc_start: 0.2979 (OUTLIER) cc_final: 0.1865 (ptt) REVERT: H 31 MET cc_start: 0.7421 (tpp) cc_final: 0.6831 (tpt) REVERT: H 216 MET cc_start: 0.7803 (mmm) cc_final: 0.7525 (mmm) REVERT: H 286 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6821 (pm20) REVERT: H 289 GLU cc_start: 0.7708 (pm20) cc_final: 0.7424 (mp0) REVERT: I 41 ASN cc_start: 0.8640 (m-40) cc_final: 0.8337 (p0) REVERT: I 91 MET cc_start: 0.5648 (tpt) cc_final: 0.5355 (tpt) REVERT: I 213 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.5155 (mp-120) outliers start: 51 outliers final: 39 residues processed: 329 average time/residue: 0.1651 time to fit residues: 87.3642 Evaluate side-chains 324 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 52 GLN Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 346 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 297 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 247 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 50 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.241756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.176266 restraints weight = 36500.943| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 3.06 r_work: 0.4118 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28420 Z= 0.099 Angle : 0.546 8.985 38590 Z= 0.277 Chirality : 0.043 0.161 3990 Planarity : 0.005 0.065 5070 Dihedral : 3.844 18.588 3900 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.42 % Allowed : 15.43 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.87 (0.14), residues: 3540 helix: 1.23 (0.17), residues: 950 sheet: -0.82 (0.18), residues: 850 loop : -1.49 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 278 TYR 0.032 0.001 TYR G 252 PHE 0.012 0.001 PHE H 234 TRP 0.051 0.001 TRP F 354 HIS 0.013 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00230 (28420) covalent geometry : angle 0.54613 (38590) hydrogen bonds : bond 0.03204 ( 1009) hydrogen bonds : angle 4.58243 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: J 125 TRP cc_start: 0.5333 (m-10) cc_final: 0.5088 (m-10) REVERT: J 138 GLU cc_start: 0.8247 (pt0) cc_final: 0.7978 (mt-10) REVERT: J 352 ILE cc_start: 0.7893 (tp) cc_final: 0.7688 (tp) REVERT: A 31 MET cc_start: 0.7428 (tpp) cc_final: 0.7183 (tpt) REVERT: A 286 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6783 (pm20) REVERT: A 319 ARG cc_start: 0.7413 (mtp85) cc_final: 0.7148 (mtp85) REVERT: C 125 TRP cc_start: 0.5689 (m-10) cc_final: 0.5403 (m-10) REVERT: C 222 GLU cc_start: 0.7898 (tt0) cc_final: 0.7515 (tt0) REVERT: C 316 ARG cc_start: 0.6928 (ttp80) cc_final: 0.6256 (tmm-80) REVERT: D 107 ARG cc_start: 0.5413 (OUTLIER) cc_final: 0.5173 (ttt180) REVERT: D 129 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6356 (pt0) REVERT: D 213 GLN cc_start: 0.6308 (OUTLIER) cc_final: 0.4929 (mp-120) REVERT: E 31 MET cc_start: 0.7474 (tpp) cc_final: 0.6887 (tpt) REVERT: E 257 MET cc_start: 0.5428 (mtp) cc_final: 0.4338 (mtp) REVERT: E 319 ARG cc_start: 0.7584 (ttp-170) cc_final: 0.6980 (mtm-85) REVERT: E 326 LYS cc_start: 0.7824 (pttt) cc_final: 0.7241 (ptpt) REVERT: F 31 MET cc_start: 0.7299 (tpp) cc_final: 0.6995 (tpt) REVERT: F 131 GLU cc_start: 0.7946 (pm20) cc_final: 0.7379 (pm20) REVERT: G 31 MET cc_start: 0.7390 (tpp) cc_final: 0.6983 (tpt) REVERT: G 216 MET cc_start: 0.7676 (mmm) cc_final: 0.7421 (mmm) REVERT: H 1 MET cc_start: 0.2983 (OUTLIER) cc_final: 0.1811 (ptt) REVERT: H 31 MET cc_start: 0.7386 (tpp) cc_final: 0.6969 (tpt) REVERT: H 286 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6663 (pm20) REVERT: H 289 GLU cc_start: 0.7691 (pm20) cc_final: 0.7398 (mp0) REVERT: I 91 MET cc_start: 0.5538 (tpt) cc_final: 0.5250 (tpt) REVERT: I 213 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.5243 (mp-120) outliers start: 41 outliers final: 27 residues processed: 336 average time/residue: 0.1763 time to fit residues: 94.7887 Evaluate side-chains 311 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 52 GLN Chi-restraints excluded: chain I residue 213 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 324 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 190 optimal weight: 0.0370 chunk 7 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 318 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 323 optimal weight: 6.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 197 GLN C 41 ASN C 175 HIS ** I 175 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 = 0.4722 r_free = 0.4722 target = 0.218870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.169475 restraints weight = 34631.711| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 3.40 r_work: 0.4132 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28420 Z= 0.098 Angle : 0.548 8.878 38590 Z= 0.277 Chirality : 0.044 0.224 3990 Planarity : 0.005 0.065 5070 Dihedral : 3.751 18.079 3900 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.38 % Allowed : 15.61 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3540 helix: 1.22 (0.17), residues: 950 sheet: -0.76 (0.18), residues: 850 loop : -1.44 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 278 TYR 0.027 0.001 TYR G 252 PHE 0.010 0.001 PHE H 234 TRP 0.051 0.001 TRP F 354 HIS 0.012 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00229 (28420) covalent geometry : angle 0.54784 (38590) hydrogen bonds : bond 0.03201 ( 1009) hydrogen bonds : angle 4.56968 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 125 TRP cc_start: 0.5341 (m-10) cc_final: 0.5077 (m-10) REVERT: J 138 GLU cc_start: 0.8262 (pt0) cc_final: 0.8008 (mt-10) REVERT: A 286 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6621 (pm20) REVERT: A 319 ARG cc_start: 0.7382 (mtp85) cc_final: 0.7118 (mtp85) REVERT: C 125 TRP cc_start: 0.5556 (m-10) cc_final: 0.5272 (m-10) REVERT: C 222 GLU cc_start: 0.7903 (tt0) cc_final: 0.7516 (tt0) REVERT: D 107 ARG cc_start: 0.5420 (ttt180) cc_final: 0.5194 (ttt180) REVERT: D 129 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6388 (pt0) REVERT: D 213 GLN cc_start: 0.6344 (OUTLIER) cc_final: 0.4985 (mp-120) REVERT: E 31 MET cc_start: 0.7493 (tpp) cc_final: 0.6960 (tpt) REVERT: E 131 GLU cc_start: 0.7919 (pm20) cc_final: 0.7414 (pm20) REVERT: E 319 ARG cc_start: 0.7549 (ttp-170) cc_final: 0.6957 (mtm-85) REVERT: E 326 LYS cc_start: 0.7789 (pttt) cc_final: 0.7222 (ptpt) REVERT: F 31 MET cc_start: 0.7300 (tpp) cc_final: 0.7054 (tpt) REVERT: F 131 GLU cc_start: 0.7947 (pm20) cc_final: 0.7379 (pm20) REVERT: G 31 MET cc_start: 0.7347 (tpp) cc_final: 0.7009 (tpt) REVERT: G 216 MET cc_start: 0.7644 (mmm) cc_final: 0.7362 (mmm) REVERT: G 326 LYS cc_start: 0.7893 (pttt) cc_final: 0.7256 (ptpt) REVERT: H 1 MET cc_start: 0.2922 (OUTLIER) cc_final: 0.1741 (ptt) REVERT: H 31 MET cc_start: 0.7401 (tpp) cc_final: 0.7018 (tpt) REVERT: H 286 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6556 (pm20) REVERT: I 91 MET cc_start: 0.5558 (tpt) cc_final: 0.5271 (tpt) REVERT: I 123 GLU cc_start: 0.8518 (mp0) cc_final: 0.8165 (mp0) REVERT: I 213 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.5197 (mp-120) outliers start: 40 outliers final: 32 residues processed: 328 average time/residue: 0.1783 time to fit residues: 93.0844 Evaluate side-chains 316 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 284 TYR Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 213 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 241 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 325 optimal weight: 9.9990 chunk 155 optimal weight: 0.0040 chunk 156 optimal weight: 0.3980 chunk 237 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 197 GLN C 41 ASN ** C 175 HIS ** 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 = 0.4700 r_free = 0.4700 target = 0.216389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.167981 restraints weight = 34566.580| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.20 r_work: 0.4090 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28420 Z= 0.117 Angle : 0.563 11.411 38590 Z= 0.286 Chirality : 0.044 0.204 3990 Planarity : 0.005 0.066 5070 Dihedral : 3.866 18.730 3900 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.35 % Allowed : 15.92 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3540 helix: 1.20 (0.17), residues: 950 sheet: -0.78 (0.18), residues: 850 loop : -1.45 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 278 TYR 0.025 0.001 TYR G 252 PHE 0.012 0.001 PHE F 329 TRP 0.048 0.001 TRP F 354 HIS 0.016 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00279 (28420) covalent geometry : angle 0.56327 (38590) hydrogen bonds : bond 0.03398 ( 1009) hydrogen bonds : angle 4.61146 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 290 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 125 TRP cc_start: 0.5427 (m-10) cc_final: 0.5141 (m-10) REVERT: J 138 GLU cc_start: 0.8205 (pt0) cc_final: 0.8004 (mt-10) REVERT: A 286 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6646 (pm20) REVERT: A 319 ARG cc_start: 0.7357 (mtp85) cc_final: 0.7101 (mtp85) REVERT: C 125 TRP cc_start: 0.5552 (m-10) cc_final: 0.5288 (m-10) REVERT: C 222 GLU cc_start: 0.7856 (tt0) cc_final: 0.7477 (tt0) REVERT: D 107 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5194 (ttt180) REVERT: D 129 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6399 (pt0) REVERT: D 213 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5065 (mp-120) REVERT: E 31 MET cc_start: 0.7440 (tpp) cc_final: 0.6875 (tpt) REVERT: E 131 GLU cc_start: 0.7917 (pm20) cc_final: 0.7431 (pm20) REVERT: E 319 ARG cc_start: 0.7532 (ttp-170) cc_final: 0.7099 (mtm-85) REVERT: E 326 LYS cc_start: 0.7891 (pttt) cc_final: 0.7325 (ptpt) REVERT: F 31 MET cc_start: 0.7298 (tpp) cc_final: 0.7014 (tpt) REVERT: G 31 MET cc_start: 0.7353 (tpp) cc_final: 0.6989 (tpt) REVERT: G 216 MET cc_start: 0.7645 (mmm) cc_final: 0.7406 (mmm) REVERT: G 257 MET cc_start: 0.5281 (mtp) cc_final: 0.5066 (mtm) REVERT: H 1 MET cc_start: 0.2953 (OUTLIER) cc_final: 0.1767 (ptt) REVERT: H 31 MET cc_start: 0.7396 (tpp) cc_final: 0.7005 (tpt) REVERT: H 131 GLU cc_start: 0.7704 (pm20) cc_final: 0.7432 (pm20) REVERT: H 286 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6632 (pm20) REVERT: H 289 GLU cc_start: 0.7747 (pm20) cc_final: 0.7451 (mp0) REVERT: I 41 ASN cc_start: 0.8638 (m-40) cc_final: 0.8345 (p0) REVERT: I 91 MET cc_start: 0.5620 (tpt) cc_final: 0.5354 (tpt) REVERT: I 123 GLU cc_start: 0.8498 (mp0) cc_final: 0.8157 (mp0) REVERT: I 213 GLN cc_start: 0.6570 (OUTLIER) cc_final: 0.5194 (mp-120) REVERT: I 221 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7578 (tp) outliers start: 39 outliers final: 30 residues processed: 322 average time/residue: 0.1783 time to fit residues: 91.4484 Evaluate side-chains 319 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 233 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 278 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 317 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 260 optimal weight: 0.0060 chunk 87 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 180 optimal weight: 0.0060 overall best weight: 0.7816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 197 GLN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.218020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.168132 restraints weight = 34265.255| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 3.45 r_work: 0.4119 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28420 Z= 0.103 Angle : 0.555 11.278 38590 Z= 0.281 Chirality : 0.044 0.195 3990 Planarity : 0.005 0.067 5070 Dihedral : 3.790 18.831 3900 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.35 % Allowed : 16.06 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3540 helix: 1.19 (0.17), residues: 950 sheet: -0.76 (0.18), residues: 850 loop : -1.42 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 278 TYR 0.026 0.001 TYR G 252 PHE 0.010 0.001 PHE F 329 TRP 0.046 0.001 TRP F 354 HIS 0.020 0.001 HIS J 175 Details of bonding type rmsd covalent geometry : bond 0.00243 (28420) covalent geometry : angle 0.55485 (38590) hydrogen bonds : bond 0.03230 ( 1009) hydrogen bonds : angle 4.55967 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6201.62 seconds wall clock time: 107 minutes 7.38 seconds (6427.38 seconds total)