Starting phenix.real_space_refine on Tue Jun 24 08:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ock_12809/06_2025/7ock_12809.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ock_12809/06_2025/7ock_12809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ock_12809/06_2025/7ock_12809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ock_12809/06_2025/7ock_12809.map" model { file = "/net/cci-nas-00/data/ceres_data/7ock_12809/06_2025/7ock_12809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ock_12809/06_2025/7ock_12809.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 136 5.16 5 C 17822 2.51 5 N 4884 2.21 5 O 5434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 217 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28276 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "C" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "D" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "E" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "F" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "G" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "H" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "I" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "L" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1194 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 6, 'TRANS': 145} Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1186 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "K" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1164 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Chain: "J" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1174 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 1 Time building chain proxies: 17.05, per 1000 atoms: 0.60 Number of scatterers: 28276 At special positions: 0 Unit cell: (105.6, 124.3, 261.8, 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 136 16.00 O 5434 8.00 N 4884 7.00 C 17822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 56 " - pdb=" SG CYS L 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS K 56 " - pdb=" SG CYS K 139 " distance=2.04 Simple disulfide: pdb=" SG CYS J 56 " - pdb=" SG CYS J 139 " distance=2.04 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: 7.33 Conformation dependent library (CDL) restraints added in 3.8 seconds 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6708 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 44 sheets defined 37.9% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'B' and resid 14 through 34 Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.768A pdb=" N ILE B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.576A pdb=" N THR B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.995A pdb=" N MET B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.753A pdb=" N ASP B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 288 removed outlier: 3.856A pdb=" N SER B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.839A pdb=" N ALA B 356 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.630A pdb=" N ALA B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 34 Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.763A pdb=" N ILE C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 removed outlier: 3.680A pdb=" N VAL C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.636A pdb=" N GLY C 155 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.528A pdb=" N ILE C 206 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.601A pdb=" N THR C 250 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 289 removed outlier: 3.563A pdb=" N SER C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 352 through 356 removed outlier: 4.090A pdb=" N ALA C 356 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 371 through 380 removed outlier: 4.269A pdb=" N LEU C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 34 Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.245A pdb=" N GLN D 104 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 154 removed outlier: 3.629A pdb=" N THR D 139 " --> pdb=" O PRO D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 233 through 238 removed outlier: 4.098A pdb=" N GLY D 237 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 238' Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 269 through 288 removed outlier: 3.889A pdb=" N SER D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'D' and resid 336 through 345 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.614A pdb=" N THR D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 371 No H-bonds generated for 'chain 'D' and resid 370 through 371' Processing helix chain 'D' and resid 372 through 380 removed outlier: 3.700A pdb=" N ALA D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 34 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.591A pdb=" N ILE E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 135 through 155 Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 206 through 211 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.807A pdb=" N MET E 236 " --> pdb=" O GLY E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.750A pdb=" N THR E 250 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 288 removed outlier: 3.791A pdb=" N SER E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 Processing helix chain 'E' and resid 336 through 345 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.543A pdb=" N THR E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 370 through 380 removed outlier: 4.132A pdb=" N GLN E 374 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU E 375 " --> pdb=" O ASP E 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 34 Processing helix chain 'F' and resid 63 through 76 removed outlier: 3.627A pdb=" N ILE F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 83 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'F' and resid 135 through 155 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 206 through 211 Processing helix chain 'F' and resid 245 through 250 removed outlier: 4.313A pdb=" N ASP F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 250' Processing helix chain 'F' and resid 269 through 289 removed outlier: 3.610A pdb=" N SER F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 333 removed outlier: 3.518A pdb=" N PHE F 333 " --> pdb=" O VAL F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 345 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.976A pdb=" N THR F 354 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 369 Processing helix chain 'F' and resid 370 through 371 No H-bonds generated for 'chain 'F' and resid 370 through 371' Processing helix chain 'F' and resid 372 through 380 Processing helix chain 'G' and resid 14 through 34 Processing helix chain 'G' and resid 63 through 76 removed outlier: 3.590A pdb=" N ILE G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 83 Processing helix chain 'G' and resid 99 through 108 removed outlier: 4.090A pdb=" N ASN G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 154 removed outlier: 3.850A pdb=" N THR G 139 " --> pdb=" O PRO G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 Processing helix chain 'G' and resid 206 through 211 Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 245 through 251 Processing helix chain 'G' and resid 269 through 288 removed outlier: 3.939A pdb=" N SER G 273 " --> pdb=" O LYS G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 336 through 345 Processing helix chain 'G' and resid 371 through 381 removed outlier: 4.301A pdb=" N LEU G 375 " --> pdb=" O ASP G 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 381 " --> pdb=" O ARG G 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 34 Processing helix chain 'H' and resid 63 through 76 Processing helix chain 'H' and resid 80 through 83 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 135 through 154 Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 206 through 211 Processing helix chain 'H' and resid 233 through 238 removed outlier: 3.791A pdb=" N GLY H 237 " --> pdb=" O GLY H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 250 Processing helix chain 'H' and resid 269 through 288 Processing helix chain 'H' and resid 321 through 333 Processing helix chain 'H' and resid 336 through 345 Processing helix chain 'H' and resid 350 through 356 removed outlier: 4.258A pdb=" N ALA H 356 " --> pdb=" O LYS H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 380 Processing helix chain 'I' and resid 14 through 34 Processing helix chain 'I' and resid 63 through 76 removed outlier: 3.748A pdb=" N ILE I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 106 Processing helix chain 'I' and resid 135 through 154 Processing helix chain 'I' and resid 194 through 206 Processing helix chain 'I' and resid 206 through 211 Processing helix chain 'I' and resid 245 through 250 Processing helix chain 'I' and resid 269 through 288 removed outlier: 3.743A pdb=" N SER I 273 " --> pdb=" O LYS I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 333 Processing helix chain 'I' and resid 336 through 345 Processing helix chain 'I' and resid 350 through 355 Processing helix chain 'I' and resid 365 through 369 removed outlier: 3.517A pdb=" N GLU I 368 " --> pdb=" O PHE I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 380 Processing helix chain 'L' and resid 23 through 41 removed outlier: 3.520A pdb=" N MET L 28 " --> pdb=" O ASP L 24 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 79 through 92 Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.959A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'K' and resid 24 through 41 Processing helix chain 'K' and resid 79 through 92 Processing helix chain 'J' and resid 23 through 41 Processing helix chain 'J' and resid 41 through 46 Processing helix chain 'J' and resid 79 through 92 Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 10 removed outlier: 5.393A pdb=" N ARG B 161 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N HIS B 189 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP B 163 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 187 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS B 165 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 185 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN B 167 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 183 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 169 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 179 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP B 173 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 45 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 45 removed outlier: 7.008A pdb=" N GLY B 96 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY B 54 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN B 98 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 56 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 127 removed outlier: 3.566A pdb=" N SER B 309 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 10 removed outlier: 5.849A pdb=" N ARG C 161 " --> pdb=" O HIS C 189 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS C 189 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP C 163 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR C 187 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS C 165 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU C 185 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN C 167 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 183 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR C 169 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 179 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP C 173 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 45 Processing sheet with id=AA8, first strand: chain 'C' and resid 38 through 45 removed outlier: 7.326A pdb=" N GLY C 96 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY C 54 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLN C 98 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 56 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'C' and resid 120 through 127 removed outlier: 3.779A pdb=" N SER C 309 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 10 removed outlier: 4.143A pdb=" N GLN D 188 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP D 163 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER D 186 " --> pdb=" O ASP D 163 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS D 165 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 184 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN D 167 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA D 182 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR D 169 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE D 180 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN D 171 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 38 through 45 removed outlier: 6.745A pdb=" N VAL D 50 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA D 94 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL D 52 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY D 96 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY D 54 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 78 through 79 Processing sheet with id=AB5, first strand: chain 'D' and resid 120 through 127 Processing sheet with id=AB6, first strand: chain 'E' and resid 3 through 10 removed outlier: 3.799A pdb=" N GLN E 188 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP E 163 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER E 186 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS E 165 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL E 184 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLN E 167 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA E 182 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR E 169 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE E 180 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN E 171 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 90 through 98 removed outlier: 6.655A pdb=" N VAL E 50 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA E 94 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL E 52 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY E 96 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY E 54 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN E 98 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE E 56 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 120 through 127 Processing sheet with id=AB9, first strand: chain 'F' and resid 2 through 10 removed outlier: 5.997A pdb=" N ARG F 161 " --> pdb=" O HIS F 189 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS F 189 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP F 163 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR F 187 " --> pdb=" O ASP F 163 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS F 165 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU F 185 " --> pdb=" O LYS F 165 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN F 167 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL F 183 " --> pdb=" O GLN F 167 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR F 169 " --> pdb=" O ASP F 181 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY F 179 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP F 173 " --> pdb=" O ILE F 177 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 90 through 94 removed outlier: 4.059A pdb=" N GLY F 54 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.734A pdb=" N HIS F 79 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 84 " --> pdb=" O HIS F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 120 through 127 Processing sheet with id=AC4, first strand: chain 'G' and resid 2 through 10 removed outlier: 7.034A pdb=" N ASP G 163 " --> pdb=" O SER G 186 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER G 186 " --> pdb=" O ASP G 163 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 165 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL G 184 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN G 167 " --> pdb=" O ALA G 182 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA G 182 " --> pdb=" O GLN G 167 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 169 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE G 180 " --> pdb=" O THR G 169 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN G 171 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LYS G 221 " --> pdb=" O GLY G 179 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP G 181 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N PHE G 223 " --> pdb=" O ASP G 181 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL G 183 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 90 through 93 Processing sheet with id=AC6, first strand: chain 'G' and resid 90 through 93 Processing sheet with id=AC7, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AC8, first strand: chain 'G' and resid 120 through 127 Processing sheet with id=AC9, first strand: chain 'H' and resid 5 through 10 removed outlier: 4.198A pdb=" N GLN H 188 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP H 163 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER H 186 " --> pdb=" O ASP H 163 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS H 165 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 184 " --> pdb=" O LYS H 165 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN H 167 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA H 182 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR H 169 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE H 180 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN H 171 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 178 " --> pdb=" O GLN H 171 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 90 through 96 removed outlier: 6.285A pdb=" N VAL H 50 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA H 94 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL H 52 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY H 96 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY H 54 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 78 through 79 Processing sheet with id=AD3, first strand: chain 'H' and resid 120 through 126 Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 10 removed outlier: 5.112A pdb=" N ASP I 163 " --> pdb=" O GLN I 188 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN I 171 " --> pdb=" O ILE I 180 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE I 180 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP I 173 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 90 through 95 Processing sheet with id=AD6, first strand: chain 'I' and resid 78 through 79 Processing sheet with id=AD7, first strand: chain 'I' and resid 120 through 127 Processing sheet with id=AD8, first strand: chain 'L' and resid 49 through 50 removed outlier: 3.965A pdb=" N LEU L 98 " --> pdb=" O VAL L 15 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 66 through 69 removed outlier: 3.501A pdb=" N ILE L 142 " --> pdb=" O PHE L 145 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.613A pdb=" N VAL A 71 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 16 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 98 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 66 through 69 removed outlier: 3.905A pdb=" N ILE A 142 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 47 through 50 Processing sheet with id=AE4, first strand: chain 'K' and resid 47 through 50 Processing sheet with id=AE5, first strand: chain 'K' and resid 126 through 129 removed outlier: 5.151A pdb=" N ARG K 148 " --> pdb=" O GLN K 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 47 through 48 removed outlier: 3.896A pdb=" N LEU J 98 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 66 through 69 Processing sheet with id=AE8, first strand: chain 'J' and resid 126 through 129 removed outlier: 4.901A pdb=" N PHE J 127 " --> pdb=" O GLN J 150 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN J 150 " --> pdb=" O PHE J 127 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3645 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: 9.54 Time building geometry restraints manager: 8.60 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: 9517 1.34 - 1.46: 5422 1.46 - 1.57: 13694 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 28849 Sorted by residual: bond pdb=" C ILE G 210 " pdb=" N LEU G 211 " ideal model delta sigma weight residual 1.331 1.285 0.046 2.07e-02 2.33e+03 4.86e+00 bond pdb=" CB PHE B 84 " pdb=" CG PHE B 84 " ideal model delta sigma weight residual 1.502 1.453 0.049 2.30e-02 1.89e+03 4.46e+00 bond pdb=" CA HIS C 189 " pdb=" CB HIS C 189 " ideal model delta sigma weight residual 1.535 1.493 0.043 2.09e-02 2.29e+03 4.15e+00 bond pdb=" CA PHE D 360 " pdb=" CB PHE D 360 " ideal model delta sigma weight residual 1.534 1.504 0.030 1.57e-02 4.06e+03 3.65e+00 bond pdb=" CB PHE A 3 " pdb=" CG PHE A 3 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.60e+00 ... (remaining 28844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 38419 2.61 - 5.22: 627 5.22 - 7.83: 43 7.83 - 10.44: 8 10.44 - 13.05: 2 Bond angle restraints: 39099 Sorted by residual: angle pdb=" N VAL H 132 " pdb=" CA VAL H 132 " pdb=" C VAL H 132 " ideal model delta sigma weight residual 112.83 106.65 6.18 9.90e-01 1.02e+00 3.90e+01 angle pdb=" CA CYS L 139 " pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " ideal model delta sigma weight residual 114.40 127.45 -13.05 2.30e+00 1.89e-01 3.22e+01 angle pdb=" N VAL I 132 " pdb=" CA VAL I 132 " pdb=" C VAL I 132 " ideal model delta sigma weight residual 111.91 107.25 4.66 8.90e-01 1.26e+00 2.75e+01 angle pdb=" CA CYS K 56 " pdb=" CB CYS K 56 " pdb=" SG CYS K 56 " ideal model delta sigma weight residual 114.40 124.54 -10.14 2.30e+00 1.89e-01 1.94e+01 angle pdb=" CA CYS L 56 " pdb=" CB CYS L 56 " pdb=" SG CYS L 56 " ideal model delta sigma weight residual 114.40 124.36 -9.96 2.30e+00 1.89e-01 1.88e+01 ... (remaining 39094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 15535 18.06 - 36.12: 1467 36.12 - 54.18: 236 54.18 - 72.24: 48 72.24 - 90.30: 42 Dihedral angle restraints: 17328 sinusoidal: 6848 harmonic: 10480 Sorted by residual: dihedral pdb=" CB CYS A 56 " pdb=" SG CYS A 56 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -0.06 -85.94 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS J 56 " pdb=" SG CYS J 56 " pdb=" SG CYS J 139 " pdb=" CB CYS J 139 " ideal model delta sinusoidal sigma weight residual -86.00 -6.41 -79.59 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CA CYS L 23 " pdb=" C CYS L 23 " pdb=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta harmonic sigma weight residual -180.00 -147.83 -32.17 0 5.00e+00 4.00e-02 4.14e+01 ... (remaining 17325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3056 0.042 - 0.085: 975 0.085 - 0.127: 290 0.127 - 0.169: 30 0.169 - 0.211: 8 Chirality restraints: 4359 Sorted by residual: chirality pdb=" CB ILE L 61 " pdb=" CA ILE L 61 " pdb=" CG1 ILE L 61 " pdb=" CG2 ILE L 61 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLU K 6 " pdb=" N GLU K 6 " pdb=" C GLU K 6 " pdb=" CB GLU K 6 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" C PRO C 162 " pdb=" CB PRO C 162 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 4356 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 123 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO L 124 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 124 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 124 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 130 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO J 131 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO J 131 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO J 131 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET G 134 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO G 135 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 135 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 135 " -0.031 5.00e-02 4.00e+02 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 675 2.57 - 3.15: 28772 3.15 - 3.74: 50507 3.74 - 4.32: 69128 4.32 - 4.90: 105435 Nonbonded interactions: 254517 Sorted by model distance: nonbonded pdb=" O TYR I 125 " pdb=" OH TYR I 251 " model vdw 1.988 3.040 nonbonded pdb=" OD1 ASP B 194 " pdb=" OG SER B 197 " model vdw 1.998 3.040 nonbonded pdb=" O GLN A 128 " pdb=" NH1 ARG A 147 " model vdw 2.018 3.120 nonbonded pdb=" OD1 ASP F 194 " pdb=" OG SER F 197 " model vdw 2.026 3.040 nonbonded pdb=" OG SER B 299 " pdb=" OG1 THR B 308 " model vdw 2.044 3.040 ... (remaining 254512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 59 or resid 65 through 153)) selection = (chain 'J' and (resid 3 through 59 or resid 65 through 153)) selection = (chain 'K' and resid 3 through 153) selection = (chain 'L' and (resid 3 through 59 or resid 65 through 153)) } ncs_group { reference = (chain 'B' and resid 1 through 383) selection = (chain 'C' and resid 1 through 383) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 1 through 383) selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 63.190 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4191 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 : 0.008 0.058 28853 Z= 0.383 Angle : 0.865 13.048 39107 Z= 0.504 Chirality : 0.045 0.211 4359 Planarity : 0.005 0.064 5118 Dihedral : 14.977 90.301 10608 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 36.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 0.20 % Allowed : 9.45 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.12), residues: 3638 helix: -2.36 (0.12), residues: 1148 sheet: -0.78 (0.17), residues: 798 loop : -2.16 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 159 HIS 0.011 0.003 HIS G 364 PHE 0.032 0.002 PHE K 140 TYR 0.027 0.003 TYR K 100 ARG 0.012 0.001 ARG G 279 Details of bonding type rmsd hydrogen bonds : bond 0.16871 ( 1297) hydrogen bonds : angle 7.64371 ( 3645) SS BOND : bond 0.00902 ( 4) SS BOND : angle 4.51196 ( 8) covalent geometry : bond 0.00767 (28849) covalent geometry : angle 0.86268 (39099) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 498 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 PRO cc_start: 0.3760 (Cg_exo) cc_final: 0.3160 (Cg_endo) REVERT: B 343 MET cc_start: 0.3541 (ttp) cc_final: 0.3271 (mtp) REVERT: E 185 LEU cc_start: 0.7472 (tp) cc_final: 0.6960 (mp) REVERT: G 185 LEU cc_start: 0.7767 (tt) cc_final: 0.7528 (mt) REVERT: I 215 TRP cc_start: 0.7380 (m-10) cc_final: 0.7026 (m-10) REVERT: I 345 ASP cc_start: 0.7996 (t0) cc_final: 0.7757 (t0) REVERT: L 28 MET cc_start: 0.9058 (mmm) cc_final: 0.8202 (tpp) REVERT: L 53 LEU cc_start: 0.5538 (tp) cc_final: 0.4845 (tp) REVERT: L 56 CYS cc_start: 0.0349 (OUTLIER) cc_final: -0.0157 (m) REVERT: L 83 ASN cc_start: 0.9242 (t0) cc_final: 0.9036 (t0) REVERT: L 87 LEU cc_start: 0.8466 (mt) cc_final: 0.8006 (mt) REVERT: L 142 ILE cc_start: 0.5470 (tt) cc_final: 0.4603 (tt) REVERT: K 12 TYR cc_start: 0.1790 (m-80) cc_final: 0.0579 (m-80) REVERT: K 13 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.6509 (m) REVERT: K 98 LEU cc_start: 0.6676 (mp) cc_final: 0.5755 (tt) REVERT: K 127 PHE cc_start: 0.5151 (t80) cc_final: 0.4344 (t80) REVERT: J 109 LEU cc_start: 0.6376 (pt) cc_final: 0.5529 (pt) outliers start: 6 outliers final: 2 residues processed: 504 average time/residue: 0.4675 time to fit residues: 351.1680 Evaluate side-chains 280 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 276 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain J residue 139 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 9.9990 chunk 274 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 chunk 328 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 359 HIS ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS C 21 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 119 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 195 GLN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN F 87 ASN F 104 GLN ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 HIS F 359 HIS G 14 HIS G 70 ASN G 79 HIS ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN G 195 GLN G 297 GLN G 374 GLN H 3 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS H 87 ASN H 98 GLN H 103 ASN H 104 GLN H 114 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 225 ASN H 257 HIS ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 HIS I 33 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 ASN ** I 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 GLN ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 152 GLN A 153 HIS K 94 GLN K 103 GLN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.058553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.046558 restraints weight = 214900.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.047803 restraints weight = 141881.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.048582 restraints weight = 100365.879| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5063 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 28853 Z= 0.227 Angle : 0.823 12.090 39107 Z= 0.433 Chirality : 0.049 0.207 4359 Planarity : 0.007 0.096 5118 Dihedral : 6.066 59.996 3964 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 3.10 % Allowed : 15.79 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3638 helix: -0.47 (0.14), residues: 1154 sheet: -0.13 (0.18), residues: 749 loop : -1.47 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 92 HIS 0.015 0.003 HIS D 14 PHE 0.026 0.003 PHE I 230 TYR 0.030 0.003 TYR E 351 ARG 0.015 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 1297) hydrogen bonds : angle 6.55085 ( 3645) SS BOND : bond 0.00273 ( 4) SS BOND : angle 2.47051 ( 8) covalent geometry : bond 0.00477 (28849) covalent geometry : angle 0.82273 (39099) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 321 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 ILE cc_start: 0.2131 (OUTLIER) cc_final: 0.1324 (pt) REVERT: B 343 MET cc_start: 0.3374 (ttp) cc_final: 0.2924 (mtp) REVERT: D 246 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6352 (mt) REVERT: D 365 PHE cc_start: 0.1162 (m-80) cc_final: 0.0821 (m-80) REVERT: E 353 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.5105 (pt0) REVERT: F 360 PHE cc_start: 0.6326 (m-80) cc_final: 0.6057 (m-10) REVERT: F 367 TRP cc_start: 0.7283 (p90) cc_final: 0.6397 (p90) REVERT: G 30 ILE cc_start: 0.4105 (OUTLIER) cc_final: 0.3800 (tp) REVERT: G 32 GLU cc_start: 0.8740 (tt0) cc_final: 0.8498 (mt-10) REVERT: G 46 LYS cc_start: 0.7707 (tppt) cc_final: 0.6942 (tttp) REVERT: G 185 LEU cc_start: 0.8199 (tt) cc_final: 0.7819 (mt) REVERT: H 173 ASP cc_start: 0.8985 (m-30) cc_final: 0.8659 (p0) REVERT: I 82 MET cc_start: 0.2034 (mmt) cc_final: 0.1659 (mmm) REVERT: I 134 MET cc_start: 0.1817 (mmm) cc_final: 0.1233 (mmm) REVERT: I 215 TRP cc_start: 0.7788 (m-10) cc_final: 0.7337 (m-10) REVERT: I 345 ASP cc_start: 0.8086 (t0) cc_final: 0.7656 (t0) REVERT: L 28 MET cc_start: 0.8886 (mmm) cc_final: 0.8061 (tpp) REVERT: L 34 MET cc_start: 0.6645 (mtt) cc_final: 0.6071 (mtt) REVERT: L 141 THR cc_start: -0.2519 (OUTLIER) cc_final: -0.2876 (m) REVERT: L 143 ASP cc_start: 0.8740 (t70) cc_final: 0.8299 (t70) REVERT: A 28 MET cc_start: 0.8695 (tpp) cc_final: 0.8443 (tpp) REVERT: K 127 PHE cc_start: 0.5858 (t80) cc_final: 0.5075 (t80) outliers start: 93 outliers final: 49 residues processed: 398 average time/residue: 0.4049 time to fit residues: 251.8833 Evaluate side-chains 298 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 293 ARG Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 PHE Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 139 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 214 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 124 optimal weight: 0.0170 chunk 131 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 358 optimal weight: 5.9990 chunk 330 optimal weight: 0.7980 chunk 178 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 overall best weight: 1.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS G 3 HIS ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN H 297 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.058573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.046898 restraints weight = 214604.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.048187 restraints weight = 141135.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.048972 restraints weight = 99780.102| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5109 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28853 Z= 0.153 Angle : 0.734 15.686 39107 Z= 0.373 Chirality : 0.046 0.267 4359 Planarity : 0.005 0.073 5118 Dihedral : 5.671 51.971 3962 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 3.40 % Allowed : 17.56 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3638 helix: 0.14 (0.15), residues: 1159 sheet: 0.16 (0.19), residues: 758 loop : -1.25 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 215 HIS 0.008 0.001 HIS F 359 PHE 0.026 0.002 PHE D 84 TYR 0.030 0.002 TYR D 351 ARG 0.007 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 1297) hydrogen bonds : angle 6.11091 ( 3645) SS BOND : bond 0.00129 ( 4) SS BOND : angle 2.11543 ( 8) covalent geometry : bond 0.00334 (28849) covalent geometry : angle 0.73338 (39099) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 266 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.3249 (ttp) cc_final: 0.2453 (mtp) REVERT: D 246 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6951 (mp) REVERT: D 272 ARG cc_start: 0.1476 (OUTLIER) cc_final: -0.0187 (ttp80) REVERT: E 134 MET cc_start: 0.1973 (mtp) cc_final: 0.1670 (mmm) REVERT: E 353 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5719 (pt0) REVERT: F 206 ILE cc_start: 0.7678 (mp) cc_final: 0.7461 (mp) REVERT: F 215 TRP cc_start: 0.3130 (m-10) cc_final: 0.2861 (m-10) REVERT: F 360 PHE cc_start: 0.6172 (m-80) cc_final: 0.5538 (m-10) REVERT: F 367 TRP cc_start: 0.7343 (p90) cc_final: 0.6261 (p90) REVERT: G 30 ILE cc_start: 0.4300 (OUTLIER) cc_final: 0.3971 (tp) REVERT: G 32 GLU cc_start: 0.8750 (tt0) cc_final: 0.8517 (mt-10) REVERT: G 46 LYS cc_start: 0.7742 (tppt) cc_final: 0.6617 (tttm) REVERT: G 185 LEU cc_start: 0.8268 (tt) cc_final: 0.8045 (mt) REVERT: G 203 MET cc_start: 0.2412 (tpt) cc_final: 0.2160 (mtp) REVERT: G 311 MET cc_start: 0.4142 (tmm) cc_final: 0.2819 (tpt) REVERT: H 49 MET cc_start: 0.7558 (ppp) cc_final: 0.6470 (ppp) REVERT: H 145 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7313 (m) REVERT: H 173 ASP cc_start: 0.9049 (m-30) cc_final: 0.8671 (p0) REVERT: I 215 TRP cc_start: 0.7846 (m-10) cc_final: 0.7367 (m-10) REVERT: I 345 ASP cc_start: 0.7966 (t0) cc_final: 0.7758 (t0) REVERT: L 28 MET cc_start: 0.8832 (mmm) cc_final: 0.8025 (tpp) REVERT: L 139 CYS cc_start: 0.0931 (OUTLIER) cc_final: -0.1033 (m) REVERT: L 143 ASP cc_start: 0.8604 (t70) cc_final: 0.8190 (t70) REVERT: K 78 LYS cc_start: 0.7487 (tmtt) cc_final: 0.6997 (mmtt) outliers start: 102 outliers final: 48 residues processed: 348 average time/residue: 0.4125 time to fit residues: 226.4639 Evaluate side-chains 282 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 92 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 139 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 245 optimal weight: 0.6980 chunk 330 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 257 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 163 optimal weight: 30.0000 chunk 296 optimal weight: 9.9990 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN C 79 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.056594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.044986 restraints weight = 219686.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.046151 restraints weight = 148419.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.046907 restraints weight = 106094.429| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 28853 Z= 0.228 Angle : 0.817 17.392 39107 Z= 0.422 Chirality : 0.048 0.242 4359 Planarity : 0.006 0.073 5118 Dihedral : 5.945 51.753 3962 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 30.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.33 % Favored : 94.53 % Rotamer: Outliers : 4.57 % Allowed : 18.76 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3638 helix: -0.08 (0.14), residues: 1173 sheet: -0.35 (0.18), residues: 759 loop : -1.33 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 92 HIS 0.026 0.002 HIS F 359 PHE 0.032 0.003 PHE D 360 TYR 0.027 0.003 TYR C 351 ARG 0.010 0.001 ARG E 152 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 1297) hydrogen bonds : angle 6.44211 ( 3645) SS BOND : bond 0.00244 ( 4) SS BOND : angle 1.82891 ( 8) covalent geometry : bond 0.00502 (28849) covalent geometry : angle 0.81638 (39099) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 278 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.5400 (t80) REVERT: B 310 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.3865 (pt) REVERT: B 343 MET cc_start: 0.3650 (ttp) cc_final: 0.2812 (mtp) REVERT: C 43 THR cc_start: 0.3251 (OUTLIER) cc_final: 0.1989 (p) REVERT: D 236 MET cc_start: 0.0644 (ttt) cc_final: 0.0255 (tpt) REVERT: D 246 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7259 (mp) REVERT: E 51 LEU cc_start: 0.8339 (tt) cc_final: 0.8105 (mm) REVERT: E 353 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5790 (pt0) REVERT: F 5 PHE cc_start: 0.6356 (t80) cc_final: 0.6150 (t80) REVERT: F 30 ILE cc_start: 0.6918 (tp) cc_final: 0.6607 (tp) REVERT: F 206 ILE cc_start: 0.7620 (mp) cc_final: 0.7415 (mp) REVERT: F 236 MET cc_start: 0.6440 (mtt) cc_final: 0.6197 (mmt) REVERT: F 330 ARG cc_start: 0.6423 (mtm110) cc_final: 0.6194 (mmt90) REVERT: F 359 HIS cc_start: 0.5644 (m170) cc_final: 0.5240 (m170) REVERT: F 367 TRP cc_start: 0.7402 (p90) cc_final: 0.6839 (p90) REVERT: G 30 ILE cc_start: 0.4710 (OUTLIER) cc_final: 0.4432 (tp) REVERT: G 32 GLU cc_start: 0.8846 (tt0) cc_final: 0.8602 (mt-10) REVERT: G 46 LYS cc_start: 0.7906 (tppt) cc_final: 0.6343 (tttp) REVERT: G 49 MET cc_start: 0.7971 (ttp) cc_final: 0.7711 (mtt) REVERT: G 203 MET cc_start: 0.3165 (tpt) cc_final: 0.2890 (mtp) REVERT: G 311 MET cc_start: 0.4817 (tmm) cc_final: 0.3579 (tpt) REVERT: G 343 MET cc_start: 0.5559 (ptt) cc_final: 0.5318 (ptt) REVERT: H 14 HIS cc_start: 0.8015 (m-70) cc_final: 0.7776 (m-70) REVERT: H 89 CYS cc_start: 0.6955 (t) cc_final: 0.6620 (m) REVERT: H 145 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.7138 (m) REVERT: H 173 ASP cc_start: 0.9015 (m-30) cc_final: 0.8607 (p0) REVERT: I 215 TRP cc_start: 0.8106 (m-10) cc_final: 0.7675 (m-10) REVERT: I 236 MET cc_start: 0.6686 (ptm) cc_final: 0.6425 (ptm) REVERT: I 254 MET cc_start: 0.6070 (tpt) cc_final: 0.4835 (tmm) REVERT: I 345 ASP cc_start: 0.7994 (t0) cc_final: 0.7778 (t0) REVERT: L 28 MET cc_start: 0.8664 (mmm) cc_final: 0.7853 (tpp) REVERT: L 101 LYS cc_start: 0.7402 (mttt) cc_final: 0.7159 (ttpt) REVERT: A 12 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.5189 (t80) REVERT: K 13 VAL cc_start: 0.7935 (OUTLIER) cc_final: 0.6599 (t) REVERT: K 78 LYS cc_start: 0.7863 (tmtt) cc_final: 0.7439 (mmtt) REVERT: K 89 CYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6827 (p) REVERT: J 34 MET cc_start: 0.6276 (mtt) cc_final: 0.3865 (mtt) REVERT: J 109 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6206 (pt) REVERT: J 121 GLU cc_start: 0.0475 (mm-30) cc_final: -0.0102 (mm-30) outliers start: 137 outliers final: 63 residues processed: 394 average time/residue: 0.4098 time to fit residues: 257.9334 Evaluate side-chains 304 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 PHE Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 168 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 303 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 243 optimal weight: 0.0670 chunk 71 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN C 3 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS F 119 GLN ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS G 70 ASN ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN K 103 GLN K 150 GLN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.056845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.045204 restraints weight = 214078.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.046419 restraints weight = 144413.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.047100 restraints weight = 101940.594| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 28853 Z= 0.157 Angle : 0.733 15.526 39107 Z= 0.372 Chirality : 0.046 0.182 4359 Planarity : 0.005 0.062 5118 Dihedral : 5.610 43.743 3961 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 3.60 % Allowed : 20.79 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3638 helix: 0.23 (0.15), residues: 1166 sheet: -0.20 (0.18), residues: 758 loop : -1.28 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 159 HIS 0.014 0.001 HIS L 31 PHE 0.041 0.002 PHE J 3 TYR 0.038 0.002 TYR C 140 ARG 0.006 0.001 ARG C 272 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1297) hydrogen bonds : angle 6.10216 ( 3645) SS BOND : bond 0.00722 ( 4) SS BOND : angle 3.91174 ( 8) covalent geometry : bond 0.00343 (28849) covalent geometry : angle 0.73109 (39099) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 257 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.5604 (t80) REVERT: B 49 MET cc_start: 0.2921 (tpp) cc_final: 0.2697 (mmp) REVERT: B 82 MET cc_start: -0.0920 (mmt) cc_final: -0.1250 (mmm) REVERT: B 203 MET cc_start: 0.8338 (mmm) cc_final: 0.8137 (mmm) REVERT: B 310 ILE cc_start: 0.5138 (OUTLIER) cc_final: 0.4094 (pt) REVERT: B 343 MET cc_start: 0.3928 (ttp) cc_final: 0.3110 (mtp) REVERT: C 43 THR cc_start: 0.3599 (OUTLIER) cc_final: 0.2334 (p) REVERT: D 121 LEU cc_start: 0.6287 (tt) cc_final: 0.5984 (tp) REVERT: D 122 MET cc_start: 0.5330 (mtm) cc_final: 0.4844 (mtt) REVERT: D 246 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6742 (mp) REVERT: D 298 VAL cc_start: 0.8581 (t) cc_final: 0.8273 (p) REVERT: E 236 MET cc_start: 0.3409 (mmt) cc_final: 0.3191 (mmt) REVERT: E 353 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6267 (pt0) REVERT: F 49 MET cc_start: 0.4705 (ppp) cc_final: 0.4153 (mmm) REVERT: F 206 ILE cc_start: 0.7692 (mp) cc_final: 0.7482 (mp) REVERT: F 330 ARG cc_start: 0.6801 (mtm110) cc_final: 0.6572 (mmt180) REVERT: F 359 HIS cc_start: 0.5726 (OUTLIER) cc_final: 0.5299 (m-70) REVERT: G 30 ILE cc_start: 0.4583 (OUTLIER) cc_final: 0.4323 (tp) REVERT: G 32 GLU cc_start: 0.8812 (tt0) cc_final: 0.8603 (mt-10) REVERT: G 44 TYR cc_start: 0.7337 (t80) cc_final: 0.7012 (m-80) REVERT: G 46 LYS cc_start: 0.7876 (tppt) cc_final: 0.6686 (tttp) REVERT: G 311 MET cc_start: 0.5236 (tmm) cc_final: 0.4396 (tpt) REVERT: G 343 MET cc_start: 0.5795 (ptt) cc_final: 0.5549 (ptt) REVERT: H 14 HIS cc_start: 0.7923 (m-70) cc_final: 0.7673 (m-70) REVERT: H 89 CYS cc_start: 0.6949 (t) cc_final: 0.6521 (m) REVERT: H 145 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7119 (m) REVERT: H 173 ASP cc_start: 0.9011 (m-30) cc_final: 0.8576 (p0) REVERT: I 79 HIS cc_start: 0.8039 (t-170) cc_final: 0.7690 (t-90) REVERT: I 215 TRP cc_start: 0.8077 (m-10) cc_final: 0.7665 (m-10) REVERT: I 254 MET cc_start: 0.5952 (tpt) cc_final: 0.4782 (tmm) REVERT: I 345 ASP cc_start: 0.7977 (t0) cc_final: 0.7752 (t0) REVERT: L 28 MET cc_start: 0.8780 (mmm) cc_final: 0.7928 (tpp) REVERT: L 101 LYS cc_start: 0.7462 (mttt) cc_final: 0.7142 (ttpt) REVERT: L 143 ASP cc_start: 0.8840 (t70) cc_final: 0.8541 (t0) REVERT: A 12 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.5266 (t80) REVERT: K 78 LYS cc_start: 0.7999 (tmtt) cc_final: 0.7515 (mmmt) REVERT: K 89 CYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6990 (p) outliers start: 108 outliers final: 67 residues processed: 348 average time/residue: 0.4144 time to fit residues: 230.9108 Evaluate side-chains 309 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 232 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 26 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 131 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 353 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 297 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 GLN I 3 HIS ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.057373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.045869 restraints weight = 217182.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.046966 restraints weight = 147907.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.047544 restraints weight = 107523.449| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28853 Z= 0.172 Angle : 0.755 17.573 39107 Z= 0.383 Chirality : 0.046 0.233 4359 Planarity : 0.005 0.061 5118 Dihedral : 5.675 53.025 3961 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 4.31 % Allowed : 21.16 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3638 helix: 0.18 (0.14), residues: 1171 sheet: -0.34 (0.18), residues: 761 loop : -1.30 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 367 HIS 0.034 0.002 HIS F 359 PHE 0.031 0.002 PHE J 3 TYR 0.040 0.002 TYR L 57 ARG 0.010 0.001 ARG L 58 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1297) hydrogen bonds : angle 6.16062 ( 3645) SS BOND : bond 0.00769 ( 4) SS BOND : angle 5.18910 ( 8) covalent geometry : bond 0.00373 (28849) covalent geometry : angle 0.75138 (39099) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 261 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: -0.1005 (mmt) cc_final: -0.1379 (mmm) REVERT: B 203 MET cc_start: 0.8285 (mmm) cc_final: 0.7937 (mmm) REVERT: B 224 ILE cc_start: 0.6734 (mp) cc_final: 0.6524 (mp) REVERT: B 343 MET cc_start: 0.4097 (ttp) cc_final: 0.3117 (mtp) REVERT: C 5 PHE cc_start: 0.5771 (t80) cc_final: 0.5537 (t80) REVERT: C 43 THR cc_start: 0.3491 (OUTLIER) cc_final: 0.3007 (p) REVERT: C 236 MET cc_start: 0.3511 (mmm) cc_final: 0.3281 (mmm) REVERT: C 311 MET cc_start: 0.3204 (mtt) cc_final: 0.2996 (mmm) REVERT: C 333 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7635 (t80) REVERT: D 92 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5632 (mm) REVERT: D 121 LEU cc_start: 0.6147 (tt) cc_final: 0.5850 (tp) REVERT: D 122 MET cc_start: 0.5438 (mtm) cc_final: 0.5155 (mtt) REVERT: D 246 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.6927 (mp) REVERT: D 364 HIS cc_start: 0.5918 (p-80) cc_final: 0.5639 (p-80) REVERT: E 236 MET cc_start: 0.3755 (mmt) cc_final: 0.3470 (mmt) REVERT: E 353 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6737 (pt0) REVERT: F 206 ILE cc_start: 0.7850 (mp) cc_final: 0.7639 (mp) REVERT: F 359 HIS cc_start: 0.6252 (OUTLIER) cc_final: 0.5966 (m170) REVERT: G 30 ILE cc_start: 0.4864 (OUTLIER) cc_final: 0.4598 (tp) REVERT: G 32 GLU cc_start: 0.8896 (tt0) cc_final: 0.8406 (pt0) REVERT: G 44 TYR cc_start: 0.7677 (t80) cc_final: 0.7385 (m-80) REVERT: G 46 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.6757 (tttm) REVERT: G 203 MET cc_start: 0.4315 (tpt) cc_final: 0.3565 (mtp) REVERT: G 311 MET cc_start: 0.5420 (tmm) cc_final: 0.4704 (tpt) REVERT: G 343 MET cc_start: 0.5975 (ptt) cc_final: 0.5614 (ptt) REVERT: H 14 HIS cc_start: 0.7899 (m-70) cc_final: 0.7648 (m-70) REVERT: H 306 GLU cc_start: 0.7672 (pp20) cc_final: 0.7065 (mm-30) REVERT: I 215 TRP cc_start: 0.8256 (m-10) cc_final: 0.7863 (m-10) REVERT: I 254 MET cc_start: 0.6070 (tpt) cc_final: 0.4918 (tmm) REVERT: I 345 ASP cc_start: 0.7971 (t0) cc_final: 0.7746 (t0) REVERT: L 28 MET cc_start: 0.8732 (mmm) cc_final: 0.7893 (tpp) REVERT: L 101 LYS cc_start: 0.7518 (mttt) cc_final: 0.7193 (ttpt) REVERT: L 143 ASP cc_start: 0.8923 (t70) cc_final: 0.8640 (t0) REVERT: A 12 TYR cc_start: 0.5912 (OUTLIER) cc_final: 0.5404 (t80) REVERT: K 33 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7203 (m90) REVERT: K 89 CYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7084 (p) REVERT: J 109 LEU cc_start: 0.7067 (pt) cc_final: 0.6591 (pp) REVERT: J 149 TRP cc_start: 0.3771 (OUTLIER) cc_final: 0.2443 (p-90) outliers start: 129 outliers final: 83 residues processed: 366 average time/residue: 0.3675 time to fit residues: 218.0057 Evaluate side-chains 332 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 237 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 145 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 300 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 253 optimal weight: 50.0000 chunk 225 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS G 70 ASN ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 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 = 0.3964 r_free = 0.3964 target = 0.056640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.045024 restraints weight = 221994.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.046338 restraints weight = 149813.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.047031 restraints weight = 107773.904| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5743 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28853 Z= 0.141 Angle : 0.736 16.080 39107 Z= 0.367 Chirality : 0.046 0.268 4359 Planarity : 0.005 0.057 5118 Dihedral : 5.517 50.043 3961 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.60 % Allowed : 22.63 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3638 helix: 0.31 (0.15), residues: 1192 sheet: -0.31 (0.18), residues: 749 loop : -1.25 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 367 HIS 0.010 0.001 HIS L 31 PHE 0.032 0.002 PHE L 11 TYR 0.041 0.002 TYR L 57 ARG 0.022 0.001 ARG K 39 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1297) hydrogen bonds : angle 5.95751 ( 3645) SS BOND : bond 0.00478 ( 4) SS BOND : angle 4.10002 ( 8) covalent geometry : bond 0.00314 (28849) covalent geometry : angle 0.73374 (39099) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 250 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.8254 (mmm) cc_final: 0.7926 (mmm) REVERT: B 343 MET cc_start: 0.4075 (ttp) cc_final: 0.3253 (mtp) REVERT: C 5 PHE cc_start: 0.5785 (t80) cc_final: 0.5353 (t80) REVERT: C 45 VAL cc_start: 0.1304 (OUTLIER) cc_final: 0.1001 (t) REVERT: C 236 MET cc_start: 0.3632 (mmm) cc_final: 0.3306 (mmm) REVERT: C 311 MET cc_start: 0.3144 (mtt) cc_final: 0.2920 (mmm) REVERT: C 333 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7559 (t80) REVERT: D 62 VAL cc_start: -0.1176 (OUTLIER) cc_final: -0.1444 (m) REVERT: D 185 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7427 (mt) REVERT: D 298 VAL cc_start: 0.8575 (t) cc_final: 0.8283 (p) REVERT: D 364 HIS cc_start: 0.5983 (p-80) cc_final: 0.5454 (t70) REVERT: F 51 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8666 (mm) REVERT: F 311 MET cc_start: 0.3085 (tpp) cc_final: 0.1884 (tpt) REVERT: F 364 HIS cc_start: 0.6937 (p-80) cc_final: 0.6647 (p-80) REVERT: G 30 ILE cc_start: 0.4600 (OUTLIER) cc_final: 0.4284 (tp) REVERT: G 32 GLU cc_start: 0.8889 (tt0) cc_final: 0.8393 (pt0) REVERT: G 203 MET cc_start: 0.4248 (tpt) cc_final: 0.3577 (mtp) REVERT: G 236 MET cc_start: 0.4076 (mmt) cc_final: 0.3803 (mmt) REVERT: G 311 MET cc_start: 0.5585 (tmm) cc_final: 0.5081 (tpt) REVERT: G 343 MET cc_start: 0.6002 (ptt) cc_final: 0.5657 (ptt) REVERT: H 14 HIS cc_start: 0.7873 (m-70) cc_final: 0.7620 (m-70) REVERT: H 145 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7146 (m) REVERT: H 306 GLU cc_start: 0.7502 (pp20) cc_final: 0.7054 (mm-30) REVERT: H 336 ARG cc_start: 0.9322 (mmt-90) cc_final: 0.9026 (mpp80) REVERT: I 215 TRP cc_start: 0.8320 (m-10) cc_final: 0.8097 (m-10) REVERT: I 345 ASP cc_start: 0.8012 (t0) cc_final: 0.7748 (t0) REVERT: L 28 MET cc_start: 0.8712 (mmm) cc_final: 0.7873 (tpp) REVERT: L 101 LYS cc_start: 0.7507 (mttt) cc_final: 0.7154 (ttpt) REVERT: L 143 ASP cc_start: 0.8934 (t70) cc_final: 0.8684 (t0) REVERT: A 12 TYR cc_start: 0.5994 (OUTLIER) cc_final: 0.5491 (t80) REVERT: K 33 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7376 (m170) REVERT: K 89 CYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7258 (p) REVERT: J 12 TYR cc_start: 0.5639 (m-80) cc_final: 0.4942 (m-80) REVERT: J 75 CYS cc_start: 0.6858 (m) cc_final: 0.6605 (p) REVERT: J 109 LEU cc_start: 0.7035 (pt) cc_final: 0.6557 (pp) outliers start: 108 outliers final: 71 residues processed: 339 average time/residue: 0.3917 time to fit residues: 216.3423 Evaluate side-chains 314 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 233 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 224 ILE Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 349 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 203 optimal weight: 0.0980 chunk 197 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 174 optimal weight: 0.0020 chunk 199 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 171 GLN G 297 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.056992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.045136 restraints weight = 219711.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.046346 restraints weight = 149214.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.047115 restraints weight = 106173.825| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.7303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28853 Z= 0.134 Angle : 0.731 15.526 39107 Z= 0.363 Chirality : 0.045 0.234 4359 Planarity : 0.005 0.066 5118 Dihedral : 5.369 49.920 3961 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.07 % Allowed : 23.06 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3638 helix: 0.47 (0.15), residues: 1194 sheet: -0.25 (0.18), residues: 757 loop : -1.18 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 367 HIS 0.019 0.001 HIS L 31 PHE 0.040 0.002 PHE L 11 TYR 0.036 0.002 TYR L 57 ARG 0.013 0.001 ARG G 279 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1297) hydrogen bonds : angle 5.80199 ( 3645) SS BOND : bond 0.01012 ( 4) SS BOND : angle 4.05303 ( 8) covalent geometry : bond 0.00292 (28849) covalent geometry : angle 0.72853 (39099) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 252 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.4095 (ttp) cc_final: 0.3311 (mtp) REVERT: C 45 VAL cc_start: 0.1146 (OUTLIER) cc_final: 0.0921 (t) REVERT: C 82 MET cc_start: -0.0577 (tpp) cc_final: -0.0900 (tpp) REVERT: C 203 MET cc_start: 0.8991 (ptp) cc_final: 0.8495 (ptp) REVERT: C 236 MET cc_start: 0.3777 (mmm) cc_final: 0.3490 (mmm) REVERT: C 333 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6830 (t80) REVERT: D 62 VAL cc_start: -0.0608 (OUTLIER) cc_final: -0.0830 (m) REVERT: D 121 LEU cc_start: 0.6511 (tt) cc_final: 0.6168 (tp) REVERT: D 122 MET cc_start: 0.5340 (mtt) cc_final: 0.4754 (mtt) REVERT: D 185 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7250 (mt) REVERT: D 298 VAL cc_start: 0.8443 (t) cc_final: 0.8152 (p) REVERT: D 329 VAL cc_start: 0.8446 (t) cc_final: 0.8245 (p) REVERT: D 364 HIS cc_start: 0.5993 (p-80) cc_final: 0.5516 (t70) REVERT: E 236 MET cc_start: 0.3927 (mmt) cc_final: 0.3091 (mmt) REVERT: E 310 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4668 (mp) REVERT: F 51 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8504 (mm) REVERT: F 311 MET cc_start: 0.2706 (tpp) cc_final: 0.2460 (tpt) REVERT: F 364 HIS cc_start: 0.6859 (p-80) cc_final: 0.6523 (p-80) REVERT: F 367 TRP cc_start: 0.7691 (p90) cc_final: 0.7326 (p90) REVERT: G 30 ILE cc_start: 0.4657 (OUTLIER) cc_final: 0.4337 (tp) REVERT: G 32 GLU cc_start: 0.8819 (tt0) cc_final: 0.8370 (pt0) REVERT: G 236 MET cc_start: 0.4171 (mmt) cc_final: 0.3853 (mmt) REVERT: G 311 MET cc_start: 0.5336 (tmm) cc_final: 0.5039 (tpt) REVERT: G 343 MET cc_start: 0.5922 (ptt) cc_final: 0.5674 (ptt) REVERT: H 14 HIS cc_start: 0.7861 (m-70) cc_final: 0.7585 (m-70) REVERT: H 145 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7237 (m) REVERT: H 306 GLU cc_start: 0.7508 (pp20) cc_final: 0.7041 (mm-30) REVERT: H 336 ARG cc_start: 0.9307 (mmt-90) cc_final: 0.9026 (mpp80) REVERT: I 215 TRP cc_start: 0.8268 (m-10) cc_final: 0.7884 (m-10) REVERT: I 345 ASP cc_start: 0.7925 (t0) cc_final: 0.7656 (t0) REVERT: L 28 MET cc_start: 0.8630 (mmm) cc_final: 0.7775 (tpp) REVERT: L 101 LYS cc_start: 0.7275 (mttt) cc_final: 0.6939 (ttpt) REVERT: L 143 ASP cc_start: 0.8915 (t70) cc_final: 0.8675 (t0) REVERT: A 12 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.5440 (t80) REVERT: K 33 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7328 (m170) REVERT: K 74 ARG cc_start: 0.8495 (mtt180) cc_final: 0.7773 (mpp80) REVERT: K 89 CYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7187 (p) REVERT: J 12 TYR cc_start: 0.5753 (m-80) cc_final: 0.5185 (m-80) REVERT: J 109 LEU cc_start: 0.6801 (pt) cc_final: 0.6330 (pp) outliers start: 92 outliers final: 60 residues processed: 322 average time/residue: 0.3973 time to fit residues: 205.8036 Evaluate side-chains 305 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 234 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 116 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 281 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 224 optimal weight: 0.0670 chunk 268 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** J 105 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 = 0.3971 r_free = 0.3971 target = 0.057026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.045238 restraints weight = 219841.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.046469 restraints weight = 146891.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.047243 restraints weight = 105789.331| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.7489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28853 Z= 0.127 Angle : 0.725 15.297 39107 Z= 0.360 Chirality : 0.046 0.339 4359 Planarity : 0.005 0.064 5118 Dihedral : 5.299 47.050 3961 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.77 % Allowed : 23.56 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3638 helix: 0.62 (0.15), residues: 1190 sheet: -0.23 (0.18), residues: 776 loop : -1.14 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 367 HIS 0.020 0.001 HIS L 31 PHE 0.036 0.002 PHE D 84 TYR 0.046 0.002 TYR K 12 ARG 0.007 0.001 ARG G 279 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1297) hydrogen bonds : angle 5.69206 ( 3645) SS BOND : bond 0.00650 ( 4) SS BOND : angle 4.35183 ( 8) covalent geometry : bond 0.00283 (28849) covalent geometry : angle 0.72219 (39099) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 251 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.4078 (ttp) cc_final: 0.3108 (mtp) REVERT: C 45 VAL cc_start: 0.1113 (OUTLIER) cc_final: 0.0853 (t) REVERT: C 82 MET cc_start: -0.0589 (tpp) cc_final: -0.0908 (tpp) REVERT: C 236 MET cc_start: 0.3611 (mmm) cc_final: 0.3355 (mmm) REVERT: C 333 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6636 (t80) REVERT: D 62 VAL cc_start: -0.0433 (OUTLIER) cc_final: -0.0658 (m) REVERT: D 121 LEU cc_start: 0.6796 (tt) cc_final: 0.6359 (tp) REVERT: D 122 MET cc_start: 0.5424 (mtt) cc_final: 0.4930 (mtt) REVERT: D 185 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7259 (mt) REVERT: D 364 HIS cc_start: 0.6141 (p-80) cc_final: 0.5632 (t70) REVERT: E 236 MET cc_start: 0.4186 (mmt) cc_final: 0.3296 (mmt) REVERT: E 310 ILE cc_start: 0.5293 (OUTLIER) cc_final: 0.4925 (mp) REVERT: F 51 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8434 (mm) REVERT: F 311 MET cc_start: 0.2864 (tpp) cc_final: 0.2225 (tpt) REVERT: F 364 HIS cc_start: 0.6967 (p-80) cc_final: 0.6644 (p-80) REVERT: F 367 TRP cc_start: 0.7698 (p90) cc_final: 0.7257 (p90) REVERT: G 30 ILE cc_start: 0.4656 (OUTLIER) cc_final: 0.4336 (tp) REVERT: G 32 GLU cc_start: 0.8808 (tt0) cc_final: 0.8364 (pt0) REVERT: G 46 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.6778 (tttm) REVERT: G 131 ASP cc_start: 0.7766 (m-30) cc_final: 0.7544 (p0) REVERT: G 236 MET cc_start: 0.4475 (mmt) cc_final: 0.4183 (mmt) REVERT: G 311 MET cc_start: 0.5354 (tmm) cc_final: 0.5121 (tpt) REVERT: G 343 MET cc_start: 0.5845 (ptt) cc_final: 0.5630 (ptt) REVERT: H 14 HIS cc_start: 0.7917 (m-70) cc_final: 0.7643 (m-70) REVERT: H 306 GLU cc_start: 0.7373 (pp20) cc_final: 0.6935 (mm-30) REVERT: H 336 ARG cc_start: 0.9272 (mmt-90) cc_final: 0.8976 (mpp80) REVERT: I 215 TRP cc_start: 0.8117 (m-10) cc_final: 0.7723 (m-10) REVERT: I 345 ASP cc_start: 0.7864 (t0) cc_final: 0.7588 (t0) REVERT: L 28 MET cc_start: 0.8614 (mmm) cc_final: 0.7753 (tpp) REVERT: L 101 LYS cc_start: 0.7523 (mttt) cc_final: 0.7275 (ptmt) REVERT: L 143 ASP cc_start: 0.9013 (t70) cc_final: 0.8743 (t0) REVERT: A 12 TYR cc_start: 0.5840 (OUTLIER) cc_final: 0.5436 (t80) REVERT: K 33 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7358 (m170) REVERT: K 74 ARG cc_start: 0.8572 (mtt180) cc_final: 0.7963 (mpp80) REVERT: K 78 LYS cc_start: 0.7351 (mmtt) cc_final: 0.6777 (tptp) REVERT: K 89 CYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7115 (p) REVERT: K 140 PHE cc_start: 0.7912 (m-80) cc_final: 0.7621 (m-80) REVERT: J 12 TYR cc_start: 0.5820 (m-80) cc_final: 0.5415 (m-80) outliers start: 83 outliers final: 61 residues processed: 318 average time/residue: 0.5054 time to fit residues: 264.3249 Evaluate side-chains 301 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 229 time to evaluate : 5.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 260 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 233 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 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 = 0.3957 r_free = 0.3957 target = 0.055837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.044310 restraints weight = 226260.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.045538 restraints weight = 152317.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.046298 restraints weight = 108484.084| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.8239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28853 Z= 0.174 Angle : 0.772 15.245 39107 Z= 0.390 Chirality : 0.047 0.338 4359 Planarity : 0.006 0.105 5118 Dihedral : 5.519 47.078 3961 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.90 % Allowed : 23.66 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3638 helix: 0.50 (0.15), residues: 1171 sheet: -0.53 (0.18), residues: 787 loop : -1.23 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 367 HIS 0.027 0.002 HIS L 31 PHE 0.042 0.002 PHE D 84 TYR 0.030 0.002 TYR K 12 ARG 0.024 0.001 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 1297) hydrogen bonds : angle 5.99487 ( 3645) SS BOND : bond 0.02769 ( 4) SS BOND : angle 3.74121 ( 8) covalent geometry : bond 0.00382 (28849) covalent geometry : angle 0.77056 (39099) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 241 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.4415 (ttp) cc_final: 0.3296 (mtp) REVERT: C 45 VAL cc_start: 0.1639 (OUTLIER) cc_final: 0.1433 (t) REVERT: C 333 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7117 (t80) REVERT: D 121 LEU cc_start: 0.6852 (tt) cc_final: 0.6450 (tp) REVERT: D 122 MET cc_start: 0.5756 (mtt) cc_final: 0.5153 (mtt) REVERT: D 185 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7395 (mt) REVERT: D 364 HIS cc_start: 0.6534 (p-80) cc_final: 0.5925 (p-80) REVERT: E 236 MET cc_start: 0.4782 (mmt) cc_final: 0.3882 (mmt) REVERT: E 311 MET cc_start: 0.7674 (tmm) cc_final: 0.7261 (tmm) REVERT: E 353 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6743 (pt0) REVERT: F 51 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8509 (mm) REVERT: F 236 MET cc_start: 0.7266 (mmt) cc_final: 0.7050 (mmt) REVERT: F 330 ARG cc_start: 0.7489 (mtm110) cc_final: 0.7063 (mmt90) REVERT: F 359 HIS cc_start: 0.6491 (OUTLIER) cc_final: 0.6121 (m-70) REVERT: G 32 GLU cc_start: 0.8740 (tt0) cc_final: 0.8323 (pt0) REVERT: G 46 LYS cc_start: 0.8235 (tppt) cc_final: 0.7384 (tmtt) REVERT: G 236 MET cc_start: 0.4390 (mmt) cc_final: 0.3945 (mmm) REVERT: G 311 MET cc_start: 0.5553 (tmm) cc_final: 0.5117 (tpt) REVERT: G 343 MET cc_start: 0.6049 (ptt) cc_final: 0.5665 (ptt) REVERT: H 14 HIS cc_start: 0.8083 (m-70) cc_final: 0.7807 (m-70) REVERT: H 306 GLU cc_start: 0.7557 (pp20) cc_final: 0.7148 (mm-30) REVERT: H 336 ARG cc_start: 0.9289 (mmt-90) cc_final: 0.8977 (mpp80) REVERT: I 215 TRP cc_start: 0.8363 (m-10) cc_final: 0.8047 (m-10) REVERT: I 345 ASP cc_start: 0.8054 (t0) cc_final: 0.7850 (t0) REVERT: L 28 MET cc_start: 0.8735 (mmm) cc_final: 0.7827 (tpp) REVERT: L 143 ASP cc_start: 0.9071 (t70) cc_final: 0.8801 (t0) REVERT: A 12 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.5639 (t80) REVERT: A 109 LEU cc_start: 0.5938 (mm) cc_final: 0.5576 (tt) REVERT: K 89 CYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7156 (p) REVERT: J 109 LEU cc_start: 0.6961 (pt) cc_final: 0.6471 (pp) outliers start: 87 outliers final: 67 residues processed: 313 average time/residue: 0.3948 time to fit residues: 199.6188 Evaluate side-chains 298 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 223 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 146 optimal weight: 0.4980 chunk 251 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 257 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 228 optimal weight: 50.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.056492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.045069 restraints weight = 220404.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.046178 restraints weight = 158756.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.047031 restraints weight = 111099.421| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.8356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28853 Z= 0.139 Angle : 0.776 15.638 39107 Z= 0.382 Chirality : 0.046 0.315 4359 Planarity : 0.005 0.069 5118 Dihedral : 5.393 48.575 3961 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.20 % Allowed : 24.90 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3638 helix: 0.61 (0.15), residues: 1175 sheet: -0.39 (0.18), residues: 773 loop : -1.18 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 367 HIS 0.022 0.001 HIS F 359 PHE 0.042 0.002 PHE D 84 TYR 0.027 0.002 TYR J 12 ARG 0.009 0.001 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 1297) hydrogen bonds : angle 5.79943 ( 3645) SS BOND : bond 0.00462 ( 4) SS BOND : angle 4.86206 ( 8) covalent geometry : bond 0.00309 (28849) covalent geometry : angle 0.77270 (39099) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10358.91 seconds wall clock time: 183 minutes 59.11 seconds (11039.11 seconds total)