Starting phenix.real_space_refine on Thu Nov 20 09:51:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b40_44163/11_2025/9b40_44163.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b40_44163/11_2025/9b40_44163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b40_44163/11_2025/9b40_44163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b40_44163/11_2025/9b40_44163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b40_44163/11_2025/9b40_44163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b40_44163/11_2025/9b40_44163.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 83 5.16 5 C 20861 2.51 5 N 5612 2.21 5 O 6390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32946 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "B" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "C" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "D" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "E" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "K" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1528 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "L" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1528 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "M" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1528 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "N" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "O" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "P" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "Q" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "R" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "S" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2447 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 289 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "F" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 289 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "H" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 289 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "I" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 289 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "J" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 289 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Time building chain proxies: 7.96, per 1000 atoms: 0.24 Number of scatterers: 32946 At special positions: 0 Unit cell: (294.8, 201, 134, 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 83 16.00 O 6390 8.00 N 5612 7.00 C 20861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7842 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 50 sheets defined 28.6% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.529A pdb=" N ILE A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 176 through 198 Processing helix chain 'A' and resid 231 through 251 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 300 through 303 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.749A pdb=" N ILE B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 198 Processing helix chain 'B' and resid 231 through 251 Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 300 through 303 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 176 through 198 Processing helix chain 'C' and resid 231 through 251 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 267 through 271 removed outlier: 4.558A pdb=" N ASP C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 271' Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 300 through 303 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 162 through 169 Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 176 through 198 Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 231 through 251 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.604A pdb=" N GLU D 259 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 282 through 291 Processing helix chain 'D' and resid 300 through 303 Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.531A pdb=" N ASP D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.836A pdb=" N ILE E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 198 Processing helix chain 'E' and resid 200 through 204 Processing helix chain 'E' and resid 231 through 251 Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 267 through 271 removed outlier: 4.420A pdb=" N ASP E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 267 through 271' Processing helix chain 'E' and resid 272 through 275 Processing helix chain 'E' and resid 282 through 291 Processing helix chain 'E' and resid 300 through 303 Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'K' and resid 90 through 93 Processing helix chain 'L' and resid 33 through 37 Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.576A pdb=" N TYR L 94 " --> pdb=" O PRO L 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 37 removed outlier: 3.530A pdb=" N ALA M 36 " --> pdb=" O SER M 33 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL M 37 " --> pdb=" O LEU M 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 33 through 37' Processing helix chain 'N' and resid 99 through 105 Processing helix chain 'N' and resid 162 through 171 removed outlier: 3.819A pdb=" N ILE N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 198 Processing helix chain 'N' and resid 231 through 250 removed outlier: 3.561A pdb=" N SER N 250 " --> pdb=" O LEU N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 255 through 259 removed outlier: 3.560A pdb=" N GLU N 259 " --> pdb=" O PRO N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 275 Processing helix chain 'N' and resid 282 through 291 Processing helix chain 'N' and resid 324 through 329 Processing helix chain 'N' and resid 372 through 374 No H-bonds generated for 'chain 'N' and resid 372 through 374' Processing helix chain 'O' and resid 79 through 82 Processing helix chain 'O' and resid 162 through 169 Processing helix chain 'O' and resid 170 through 172 No H-bonds generated for 'chain 'O' and resid 170 through 172' Processing helix chain 'O' and resid 174 through 198 Processing helix chain 'O' and resid 200 through 204 removed outlier: 3.857A pdb=" N GLY O 204 " --> pdb=" O SER O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 250 Processing helix chain 'O' and resid 255 through 259 removed outlier: 3.893A pdb=" N GLU O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 269 through 275 Processing helix chain 'O' and resid 282 through 291 removed outlier: 3.526A pdb=" N TRP O 286 " --> pdb=" O SER O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 300 through 303 Processing helix chain 'O' and resid 324 through 329 removed outlier: 3.737A pdb=" N ASP O 328 " --> pdb=" O ASN O 324 " (cutoff:3.500A) Processing helix chain 'O' and resid 372 through 374 No H-bonds generated for 'chain 'O' and resid 372 through 374' Processing helix chain 'P' and resid 100 through 105 Processing helix chain 'P' and resid 162 through 170 Processing helix chain 'P' and resid 174 through 198 Processing helix chain 'P' and resid 231 through 250 removed outlier: 3.509A pdb=" N SER P 250 " --> pdb=" O LEU P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 259 removed outlier: 3.565A pdb=" N GLU P 259 " --> pdb=" O PRO P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 275 removed outlier: 3.537A pdb=" N SER P 274 " --> pdb=" O ASP P 271 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL P 275 " --> pdb=" O TYR P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 291 Processing helix chain 'P' and resid 300 through 303 Processing helix chain 'P' and resid 324 through 329 Processing helix chain 'P' and resid 372 through 374 No H-bonds generated for 'chain 'P' and resid 372 through 374' Processing helix chain 'Q' and resid 79 through 82 removed outlier: 3.516A pdb=" N PHE Q 82 " --> pdb=" O PRO Q 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 79 through 82' Processing helix chain 'Q' and resid 99 through 105 Processing helix chain 'Q' and resid 161 through 171 removed outlier: 3.513A pdb=" N GLU Q 165 " --> pdb=" O GLY Q 161 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE Q 171 " --> pdb=" O ARG Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 198 Processing helix chain 'Q' and resid 231 through 250 Processing helix chain 'Q' and resid 270 through 275 Processing helix chain 'Q' and resid 282 through 291 Processing helix chain 'Q' and resid 300 through 303 Processing helix chain 'Q' and resid 372 through 374 No H-bonds generated for 'chain 'Q' and resid 372 through 374' Processing helix chain 'R' and resid 79 through 82 Processing helix chain 'R' and resid 100 through 105 removed outlier: 3.554A pdb=" N ILE R 104 " --> pdb=" O ILE R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 171 Processing helix chain 'R' and resid 174 through 198 Processing helix chain 'R' and resid 231 through 251 Processing helix chain 'R' and resid 255 through 259 removed outlier: 3.681A pdb=" N GLU R 259 " --> pdb=" O PRO R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 271 removed outlier: 4.636A pdb=" N ASP R 271 " --> pdb=" O THR R 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 267 through 271' Processing helix chain 'R' and resid 272 through 275 Processing helix chain 'R' and resid 282 through 291 Processing helix chain 'R' and resid 300 through 303 Processing helix chain 'R' and resid 372 through 374 No H-bonds generated for 'chain 'R' and resid 372 through 374' Processing helix chain 'S' and resid 79 through 82 removed outlier: 3.504A pdb=" N PHE S 82 " --> pdb=" O PRO S 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 79 through 82' Processing helix chain 'S' and resid 100 through 105 Processing helix chain 'S' and resid 162 through 171 removed outlier: 3.630A pdb=" N ILE S 171 " --> pdb=" O ARG S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 198 Processing helix chain 'S' and resid 231 through 250 Processing helix chain 'S' and resid 270 through 275 Processing helix chain 'S' and resid 282 through 291 Processing helix chain 'S' and resid 300 through 303 Processing helix chain 'S' and resid 324 through 329 Processing helix chain 'S' and resid 372 through 374 No H-bonds generated for 'chain 'S' and resid 372 through 374' Processing helix chain 'G' and resid 289 through 302 Processing helix chain 'G' and resid 303 through 326 Processing helix chain 'F' and resid 287 through 300 Processing helix chain 'F' and resid 304 through 326 Processing helix chain 'H' and resid 287 through 301 removed outlier: 4.261A pdb=" N GLU H 301 " --> pdb=" O SER H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 326 Processing helix chain 'I' and resid 287 through 300 Processing helix chain 'I' and resid 303 through 326 Processing helix chain 'J' and resid 287 through 302 Processing helix chain 'J' and resid 303 through 326 removed outlier: 3.892A pdb=" N ILE J 312 " --> pdb=" O VAL J 308 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 326 " --> pdb=" O LEU J 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 92 removed outlier: 5.481A pdb=" N GLY E 120 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 89 " --> pdb=" O GLY E 120 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL E 122 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 91 " --> pdb=" O VAL E 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 108 removed outlier: 3.764A pdb=" N VAL A 341 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER A 338 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA A 368 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 340 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY A 364 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS A 344 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER A 362 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE A 346 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP A 360 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N LEU A 348 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N VAL A 358 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N VAL A 350 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 11.927A pdb=" N SER A 356 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 150 removed outlier: 6.659A pdb=" N GLU A 116 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU B 87 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 118 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY B 89 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLY A 120 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 11.804A pdb=" N SER B 356 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N VAL B 350 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N VAL B 358 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N LEU B 348 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP B 360 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE B 346 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER B 362 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS B 344 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY B 364 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU B 340 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA B 368 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER B 338 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP B 107 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 343 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 137 through 138 removed outlier: 3.553A pdb=" N ILE A 137 " --> pdb=" O ASP K 21 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 299 removed outlier: 6.269A pdb=" N ILE A 261 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 297 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A 263 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ALA A 299 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 265 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 315 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 276 through 277 removed outlier: 4.153A pdb=" N ILE A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 306 through 307 removed outlier: 3.618A pdb=" N GLN A 306 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 125 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 130 removed outlier: 11.871A pdb=" N SER C 356 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N VAL C 350 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N VAL C 358 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N LEU C 348 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP C 360 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE C 346 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER C 362 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS C 344 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY C 364 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU C 340 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA C 368 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER C 338 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 261 through 266 removed outlier: 6.412A pdb=" N ILE B 261 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL B 297 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU B 263 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA B 299 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 265 " --> pdb=" O ALA B 299 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 295 through 299 current: chain 'B' and resid 312 through 320 removed outlier: 5.603A pdb=" N ASP B 314 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 276 through 277 removed outlier: 4.140A pdb=" N ILE B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 141 through 150 removed outlier: 6.364A pdb=" N GLU C 116 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU D 87 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 118 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY D 89 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLY C 120 " --> pdb=" O GLY D 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 130 removed outlier: 11.795A pdb=" N SER D 356 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 10.591A pdb=" N VAL D 350 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 11.426A pdb=" N VAL D 358 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N LEU D 348 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP D 360 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE D 346 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER D 362 " --> pdb=" O LYS D 344 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS D 344 " --> pdb=" O SER D 362 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY D 364 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 340 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA D 368 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER D 338 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASP D 107 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER D 343 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 295 through 299 removed outlier: 6.256A pdb=" N ILE C 261 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL C 297 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU C 263 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ALA C 299 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU C 265 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 315 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AB8, first strand: chain 'D' and resid 116 through 125 Processing sheet with id=AB9, first strand: chain 'D' and resid 129 through 130 removed outlier: 11.883A pdb=" N SER E 356 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N VAL E 350 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 11.396A pdb=" N VAL E 358 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N LEU E 348 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASP E 360 " --> pdb=" O ILE E 346 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE E 346 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER E 362 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS E 344 " --> pdb=" O SER E 362 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY E 364 " --> pdb=" O GLN E 342 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU E 340 " --> pdb=" O ALA E 366 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA E 368 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER E 338 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 341 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 261 through 266 removed outlier: 6.331A pdb=" N ILE D 261 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL D 297 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU D 263 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA D 299 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU D 265 " --> pdb=" O ALA D 299 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 295 through 299 current: chain 'D' and resid 312 through 320 removed outlier: 5.589A pdb=" N ASP D 314 " --> pdb=" O GLY D 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 261 through 266 removed outlier: 6.291A pdb=" N ILE E 261 " --> pdb=" O ARG E 295 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL E 297 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU E 263 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA E 299 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU E 265 " --> pdb=" O ALA E 299 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 295 through 299 current: chain 'E' and resid 312 through 320 removed outlier: 5.948A pdb=" N ASP E 314 " --> pdb=" O GLY E 381 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 144 through 147 removed outlier: 5.226A pdb=" N VAL K 145 " --> pdb=" O ILE K 181 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N THR K 210 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N THR K 123 " --> pdb=" O THR K 210 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU K 117 " --> pdb=" O GLY K 89 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET K 121 " --> pdb=" O PHE K 85 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE K 85 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE K 53 " --> pdb=" O PHE K 85 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLU K 76 " --> pdb=" O ALA K 56 " (cutoff:3.500A) removed outlier: 10.850A pdb=" N SER K 75 " --> pdb=" O ALA K 26 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL K 77 " --> pdb=" O PRO K 28 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG K 30 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG K 25 " --> pdb=" O ASP K 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 61 through 62 Processing sheet with id=AC5, first strand: chain 'K' and resid 95 through 96 Processing sheet with id=AC6, first strand: chain 'K' and resid 137 through 139 Processing sheet with id=AC7, first strand: chain 'L' and resid 115 through 130 removed outlier: 6.190A pdb=" N ARG L 25 " --> pdb=" O ASP L 120 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N SER L 75 " --> pdb=" O ALA L 26 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL L 77 " --> pdb=" O PRO L 28 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG L 30 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU L 76 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY L 86 " --> pdb=" O PHE L 53 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR L 55 " --> pdb=" O PHE L 84 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE L 84 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 12.281A pdb=" N PHE L 85 " --> pdb=" O MET L 121 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N MET L 121 " --> pdb=" O PHE L 85 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU L 117 " --> pdb=" O GLY L 89 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU L 166 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY L 168 " --> pdb=" O PHE L 130 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL L 145 " --> pdb=" O ILE L 181 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR L 210 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR L 123 " --> pdb=" O THR L 210 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 61 through 62 Processing sheet with id=AC9, first strand: chain 'L' and resid 137 through 139 Processing sheet with id=AD1, first strand: chain 'M' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 18 through 21 current: chain 'M' and resid 75 through 78 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 75 through 78 current: chain 'M' and resid 115 through 131 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 115 through 131 current: chain 'M' and resid 166 through 168 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 166 through 168 current: chain 'M' and resid 205 through 210 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'M' and resid 61 through 62 Processing sheet with id=AD3, first strand: chain 'M' and resid 137 through 139 Processing sheet with id=AD4, first strand: chain 'N' and resid 84 through 92 removed outlier: 5.648A pdb=" N GLY O 120 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY N 89 " --> pdb=" O GLY O 120 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL O 122 " --> pdb=" O GLY N 89 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL N 91 " --> pdb=" O VAL O 122 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 116 through 125 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 116 through 125 current: chain 'Q' and resid 357 through 370 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'N' and resid 337 through 352 removed outlier: 6.556A pdb=" N SER N 338 " --> pdb=" O ALA N 368 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA N 368 " --> pdb=" O SER N 338 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU N 340 " --> pdb=" O ALA N 366 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY N 364 " --> pdb=" O GLN N 342 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS N 344 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER N 362 " --> pdb=" O LYS N 344 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE N 346 " --> pdb=" O ASP N 360 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP N 360 " --> pdb=" O ILE N 346 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N LEU N 348 " --> pdb=" O VAL N 358 " (cutoff:3.500A) removed outlier: 11.528A pdb=" N VAL N 358 " --> pdb=" O LEU N 348 " (cutoff:3.500A) removed outlier: 10.840A pdb=" N VAL N 350 " --> pdb=" O SER N 356 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N SER N 356 " --> pdb=" O VAL N 350 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 261 through 266 removed outlier: 6.475A pdb=" N ILE N 261 " --> pdb=" O ARG N 295 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL N 297 " --> pdb=" O ILE N 261 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU N 263 " --> pdb=" O VAL N 297 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ALA N 299 " --> pdb=" O LEU N 263 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU N 265 " --> pdb=" O ALA N 299 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 294 through 299 current: chain 'N' and resid 312 through 320 removed outlier: 5.719A pdb=" N ASP N 314 " --> pdb=" O GLY N 381 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 84 through 92 removed outlier: 5.149A pdb=" N GLY P 120 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY O 89 " --> pdb=" O GLY P 120 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL P 122 " --> pdb=" O GLY O 89 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL O 91 " --> pdb=" O VAL P 122 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 337 through 352 removed outlier: 6.520A pdb=" N SER O 338 " --> pdb=" O ALA O 368 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA O 368 " --> pdb=" O SER O 338 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU O 340 " --> pdb=" O ALA O 366 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY O 364 " --> pdb=" O GLN O 342 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS O 344 " --> pdb=" O SER O 362 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER O 362 " --> pdb=" O LYS O 344 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE O 346 " --> pdb=" O ASP O 360 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP O 360 " --> pdb=" O ILE O 346 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU O 348 " --> pdb=" O VAL O 358 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N VAL O 358 " --> pdb=" O LEU O 348 " (cutoff:3.500A) removed outlier: 10.699A pdb=" N VAL O 350 " --> pdb=" O SER O 356 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N SER O 356 " --> pdb=" O VAL O 350 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 261 through 266 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 294 through 299 current: chain 'O' and resid 312 through 320 removed outlier: 5.884A pdb=" N ASP O 314 " --> pdb=" O GLY O 381 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 84 through 92 removed outlier: 6.325A pdb=" N THR P 85 " --> pdb=" O VAL S 118 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLY S 120 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU P 87 " --> pdb=" O GLY S 120 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N VAL S 122 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N GLY P 89 " --> pdb=" O VAL S 122 " (cutoff:3.500A) removed outlier: 12.309A pdb=" N VAL P 91 " --> pdb=" O PRO S 124 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 337 through 352 removed outlier: 7.485A pdb=" N SER P 338 " --> pdb=" O CYS P 370 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N CYS P 370 " --> pdb=" O SER P 338 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU P 340 " --> pdb=" O ALA P 368 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA P 368 " --> pdb=" O LEU P 340 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLN P 342 " --> pdb=" O ALA P 366 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ALA P 366 " --> pdb=" O GLN P 342 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS P 344 " --> pdb=" O GLY P 364 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLY P 364 " --> pdb=" O LYS P 344 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP P 360 " --> pdb=" O LEU P 348 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL P 350 " --> pdb=" O VAL P 358 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL P 358 " --> pdb=" O VAL P 350 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS P 352 " --> pdb=" O SER P 356 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N SER P 356 " --> pdb=" O LYS P 352 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 294 through 299 removed outlier: 6.595A pdb=" N ALA P 315 " --> pdb=" O ALA P 266 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 306 through 307 removed outlier: 4.065A pdb=" N GLN P 306 " --> pdb=" O GLU P 313 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 141 through 150 removed outlier: 7.169A pdb=" N GLU Q 116 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU R 87 " --> pdb=" O GLU Q 116 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL Q 118 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY R 89 " --> pdb=" O VAL Q 118 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY Q 120 " --> pdb=" O GLY R 89 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 129 through 130 removed outlier: 3.562A pdb=" N GLY R 154 " --> pdb=" O ASN R 363 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN R 363 " --> pdb=" O GLY R 154 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N SER R 356 " --> pdb=" O LYS R 352 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LYS R 352 " --> pdb=" O SER R 356 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL R 358 " --> pdb=" O VAL R 350 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL R 350 " --> pdb=" O VAL R 358 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP R 360 " --> pdb=" O LEU R 348 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY R 364 " --> pdb=" O LYS R 344 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS R 344 " --> pdb=" O GLY R 364 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ALA R 366 " --> pdb=" O GLN R 342 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLN R 342 " --> pdb=" O ALA R 366 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ALA R 368 " --> pdb=" O LEU R 340 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU R 340 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N CYS R 370 " --> pdb=" O SER R 338 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N SER R 338 " --> pdb=" O CYS R 370 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASP R 107 " --> pdb=" O VAL R 341 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER R 343 " --> pdb=" O ASP R 107 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 261 through 266 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 294 through 299 current: chain 'Q' and resid 312 through 320 removed outlier: 5.742A pdb=" N ASP Q 314 " --> pdb=" O GLY Q 381 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 116 through 125 Processing sheet with id=AF1, first strand: chain 'R' and resid 294 through 299 removed outlier: 6.672A pdb=" N ALA R 315 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 306 through 307 removed outlier: 3.849A pdb=" N GLN R 306 " --> pdb=" O GLU R 313 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 152 through 161 removed outlier: 12.161A pdb=" N SER S 356 " --> pdb=" O VAL S 350 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N VAL S 350 " --> pdb=" O SER S 356 " (cutoff:3.500A) removed outlier: 11.634A pdb=" N VAL S 358 " --> pdb=" O LEU S 348 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N LEU S 348 " --> pdb=" O VAL S 358 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP S 360 " --> pdb=" O ILE S 346 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE S 346 " --> pdb=" O ASP S 360 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER S 362 " --> pdb=" O LYS S 344 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS S 344 " --> pdb=" O SER S 362 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY S 364 " --> pdb=" O GLN S 342 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU S 340 " --> pdb=" O ALA S 366 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA S 368 " --> pdb=" O SER S 338 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER S 338 " --> pdb=" O ALA S 368 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 294 through 299 removed outlier: 6.719A pdb=" N ALA S 315 " --> pdb=" O ALA S 266 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 306 through 307 removed outlier: 3.723A pdb=" N GLN S 306 " --> pdb=" O GLU S 313 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3243 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: 6.93 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7149 1.33 - 1.45: 7387 1.45 - 1.57: 18935 1.57 - 1.69: 0 1.69 - 1.81: 155 Bond restraints: 33626 Sorted by residual: bond pdb=" N ASN K 38 " pdb=" CA ASN K 38 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.24e+01 bond pdb=" C GLN M 66 " pdb=" N PRO M 67 " ideal model delta sigma weight residual 1.335 1.364 -0.029 8.70e-03 1.32e+04 1.13e+01 bond pdb=" N LEU C 83 " pdb=" CA LEU C 83 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" N VAL L 201 " pdb=" CA VAL L 201 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.25e-02 6.40e+03 9.34e+00 bond pdb=" N MET C 94 " pdb=" CA MET C 94 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.22e-02 6.72e+03 9.28e+00 ... (remaining 33621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 44424 1.95 - 3.91: 1187 3.91 - 5.86: 131 5.86 - 7.82: 27 7.82 - 9.77: 6 Bond angle restraints: 45775 Sorted by residual: angle pdb=" C GLY E 280 " pdb=" N ILE E 281 " pdb=" CA ILE E 281 " ideal model delta sigma weight residual 123.13 116.12 7.01 1.34e+00 5.57e-01 2.73e+01 angle pdb=" C MET K 32 " pdb=" CA MET K 32 " pdb=" CB MET K 32 " ideal model delta sigma weight residual 115.89 109.46 6.43 1.32e+00 5.74e-01 2.37e+01 angle pdb=" N LYS K 4 " pdb=" CA LYS K 4 " pdb=" C LYS K 4 " ideal model delta sigma weight residual 113.17 107.23 5.94 1.26e+00 6.30e-01 2.22e+01 angle pdb=" CA GLU A 311 " pdb=" CB GLU A 311 " pdb=" CG GLU A 311 " ideal model delta sigma weight residual 114.10 123.17 -9.07 2.00e+00 2.50e-01 2.05e+01 angle pdb=" C GLY D 280 " pdb=" N ILE D 281 " pdb=" CA ILE D 281 " ideal model delta sigma weight residual 122.93 117.14 5.79 1.31e+00 5.83e-01 1.95e+01 ... (remaining 45770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17253 17.93 - 35.85: 1888 35.85 - 53.78: 647 53.78 - 71.70: 169 71.70 - 89.63: 65 Dihedral angle restraints: 20022 sinusoidal: 7765 harmonic: 12257 Sorted by residual: dihedral pdb=" CD ARG I 294 " pdb=" NE ARG I 294 " pdb=" CZ ARG I 294 " pdb=" NH1 ARG I 294 " ideal model delta sinusoidal sigma weight residual 0.00 -78.86 78.86 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CD ARG J 294 " pdb=" NE ARG J 294 " pdb=" CZ ARG J 294 " pdb=" NH1 ARG J 294 " ideal model delta sinusoidal sigma weight residual 0.00 66.77 -66.77 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CD ARG F 294 " pdb=" NE ARG F 294 " pdb=" CZ ARG F 294 " pdb=" NH1 ARG F 294 " ideal model delta sinusoidal sigma weight residual 0.00 -48.50 48.50 1 1.00e+01 1.00e-02 3.24e+01 ... (remaining 20019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3993 0.056 - 0.112: 947 0.112 - 0.168: 216 0.168 - 0.225: 16 0.225 - 0.281: 4 Chirality restraints: 5176 Sorted by residual: chirality pdb=" CA THR E 277 " pdb=" N THR E 277 " pdb=" C THR E 277 " pdb=" CB THR E 277 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA THR D 277 " pdb=" N THR D 277 " pdb=" C THR D 277 " pdb=" CB THR D 277 " both_signs ideal model delta sigma weight residual False 2.53 2.80 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU B 83 " pdb=" CB LEU B 83 " pdb=" CD1 LEU B 83 " pdb=" CD2 LEU B 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 5173 not shown) Planarity restraints: 6008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 294 " 1.079 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG I 294 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG I 294 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG I 294 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG I 294 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 294 " 1.006 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG J 294 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG J 294 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 294 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 294 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 294 " -0.813 9.50e-02 1.11e+02 3.64e-01 8.07e+01 pdb=" NE ARG F 294 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG F 294 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG F 294 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 294 " -0.023 2.00e-02 2.50e+03 ... (remaining 6005 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3143 2.75 - 3.29: 31930 3.29 - 3.82: 56525 3.82 - 4.36: 66840 4.36 - 4.90: 117215 Nonbonded interactions: 275653 Sorted by model distance: nonbonded pdb=" OG SER P 282 " pdb=" OD2 ASP P 285 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS B 257 " pdb=" O MET H 302 " model vdw 2.209 3.120 nonbonded pdb=" OG SER O 282 " pdb=" OD2 ASP O 285 " model vdw 2.212 3.040 nonbonded pdb=" O ASP A 271 " pdb=" OG SER A 274 " model vdw 2.219 3.040 nonbonded pdb=" O ASP C 271 " pdb=" OG SER C 274 " model vdw 2.224 3.040 ... (remaining 275648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 31.230 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.130 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:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.004 0.056 33626 Z= 0.235 Angle : 0.720 9.769 45775 Z= 0.422 Chirality : 0.052 0.281 5176 Planarity : 0.012 0.483 6008 Dihedral : 18.159 89.630 12180 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 3.83 % Allowed : 23.31 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 4287 helix: 0.98 (0.16), residues: 1007 sheet: 0.06 (0.15), residues: 1079 loop : -0.98 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 295 TYR 0.031 0.002 TYR Q 131 PHE 0.019 0.002 PHE L 169 TRP 0.014 0.001 TRP R 227 HIS 0.003 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00438 (33626) covalent geometry : angle 0.71996 (45775) hydrogen bonds : bond 0.13941 ( 1182) hydrogen bonds : angle 6.79568 ( 3243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 416 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 109 VAL cc_start: 0.8395 (p) cc_final: 0.8108 (m) REVERT: C 255 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7048 (t0) REVERT: K 32 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8127 (ttt) REVERT: K 48 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8771 (ttm170) REVERT: K 76 GLU cc_start: 0.8431 (tt0) cc_final: 0.8221 (tt0) REVERT: K 173 SER cc_start: 0.8665 (m) cc_final: 0.8372 (m) REVERT: L 76 GLU cc_start: 0.8751 (tt0) cc_final: 0.8549 (tt0) REVERT: M 68 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8690 (mmtp) REVERT: P 123 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7070 (mt-10) REVERT: R 260 LYS cc_start: 0.8840 (mtpp) cc_final: 0.7892 (ttpp) REVERT: F 294 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6607 (ttt-90) REVERT: F 302 MET cc_start: 0.8719 (ptp) cc_final: 0.8314 (ptm) REVERT: H 301 GLU cc_start: 0.8922 (pm20) cc_final: 0.8442 (pt0) outliers start: 133 outliers final: 71 residues processed: 515 average time/residue: 0.6520 time to fit residues: 401.5844 Evaluate side-chains 449 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 374 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain K residue 32 MET Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain O residue 135 THR Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 297 VAL Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain P residue 335 SER Chi-restraints excluded: chain P residue 337 PHE Chi-restraints excluded: chain P residue 340 LEU Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 254 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 284 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain F residue 294 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.0970 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN L 47 ASN L 183 ASN N 181 GLN O 136 ASN Q 212 ASN Q 306 GLN R 115 GLN R 143 ASN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN J 295 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089078 restraints weight = 58085.428| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.29 r_work: 0.3078 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33626 Z= 0.145 Angle : 0.519 12.968 45775 Z= 0.273 Chirality : 0.044 0.167 5176 Planarity : 0.004 0.051 6008 Dihedral : 6.256 59.663 4758 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.03 % Allowed : 22.68 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4287 helix: 1.55 (0.16), residues: 1008 sheet: 0.15 (0.15), residues: 1073 loop : -0.90 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 295 TYR 0.016 0.001 TYR C 279 PHE 0.010 0.001 PHE K 118 TRP 0.009 0.001 TRP N 232 HIS 0.001 0.000 HIS M 93 Details of bonding type rmsd covalent geometry : bond 0.00343 (33626) covalent geometry : angle 0.51938 (45775) hydrogen bonds : bond 0.03810 ( 1182) hydrogen bonds : angle 5.50428 ( 3243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 397 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 172 ARG cc_start: 0.8529 (mtm180) cc_final: 0.8272 (mpt-90) REVERT: A 219 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8342 (t80) REVERT: B 172 ARG cc_start: 0.8401 (mpp-170) cc_final: 0.8102 (mpp-170) REVERT: B 219 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8421 (t80) REVERT: C 109 VAL cc_start: 0.8687 (p) cc_final: 0.8396 (m) REVERT: C 351 GLU cc_start: 0.5650 (mm-30) cc_final: 0.5415 (mm-30) REVERT: D 277 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8844 (p) REVERT: D 351 GLU cc_start: 0.5524 (mm-30) cc_final: 0.5026 (mm-30) REVERT: E 219 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8329 (t80) REVERT: E 351 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.3369 (tp30) REVERT: K 1 MET cc_start: 0.7255 (mmm) cc_final: 0.6990 (tpp) REVERT: K 141 TYR cc_start: 0.8347 (t80) cc_final: 0.8032 (t80) REVERT: K 173 SER cc_start: 0.8737 (m) cc_final: 0.8456 (m) REVERT: M 195 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8685 (pt0) REVERT: Q 307 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.5970 (mtt) REVERT: R 259 GLU cc_start: 0.8245 (tp30) cc_final: 0.7902 (tp30) REVERT: R 260 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8026 (ttpp) REVERT: S 159 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.5761 (mpt) REVERT: S 177 GLU cc_start: 0.8527 (tp30) cc_final: 0.7921 (tp30) REVERT: S 181 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8238 (mp10) REVERT: F 301 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8207 (mt-10) REVERT: F 302 MET cc_start: 0.8732 (ptp) cc_final: 0.8370 (ptm) REVERT: F 319 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7572 (mp) REVERT: H 301 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8610 (pt0) REVERT: J 307 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8408 (tt0) outliers start: 140 outliers final: 58 residues processed: 493 average time/residue: 0.7018 time to fit residues: 413.1084 Evaluate side-chains 447 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 377 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 129 ILE Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 191 SER Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 324 ASN Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 340 LEU Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 94 MET Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain S residue 331 THR Chi-restraints excluded: chain S residue 340 LEU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain H residue 301 GLU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 415 optimal weight: 0.9980 chunk 126 optimal weight: 0.2980 chunk 169 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 253 GLN C 253 GLN L 208 GLN O 136 ASN Q 212 ASN R 143 ASN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.107139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089185 restraints weight = 57027.956| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.26 r_work: 0.3091 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33626 Z= 0.115 Angle : 0.483 10.973 45775 Z= 0.254 Chirality : 0.043 0.201 5176 Planarity : 0.003 0.047 6008 Dihedral : 5.209 59.812 4678 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.61 % Allowed : 22.48 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 4287 helix: 1.81 (0.16), residues: 1003 sheet: 0.17 (0.15), residues: 1075 loop : -0.82 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 206 TYR 0.014 0.001 TYR M 55 PHE 0.011 0.001 PHE K 118 TRP 0.010 0.001 TRP N 232 HIS 0.002 0.000 HIS M 93 Details of bonding type rmsd covalent geometry : bond 0.00271 (33626) covalent geometry : angle 0.48307 (45775) hydrogen bonds : bond 0.03319 ( 1182) hydrogen bonds : angle 5.18169 ( 3243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 370 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 219 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8458 (t80) REVERT: B 172 ARG cc_start: 0.8386 (mpp-170) cc_final: 0.8015 (mpp-170) REVERT: B 288 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8889 (tp30) REVERT: C 98 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8564 (mtm180) REVERT: C 109 VAL cc_start: 0.8715 (p) cc_final: 0.8422 (m) REVERT: C 310 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: D 196 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.9228 (m-80) REVERT: D 267 THR cc_start: 0.9322 (t) cc_final: 0.8837 (m) REVERT: D 351 GLU cc_start: 0.5524 (mm-30) cc_final: 0.4987 (mm-30) REVERT: E 219 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8513 (t80) REVERT: E 285 ASP cc_start: 0.8756 (t70) cc_final: 0.8447 (t0) REVERT: E 351 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.3365 (tp30) REVERT: K 1 MET cc_start: 0.7321 (mmm) cc_final: 0.7095 (tpp) REVERT: K 141 TYR cc_start: 0.8323 (t80) cc_final: 0.7951 (t80) REVERT: N 167 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7927 (mmt-90) REVERT: Q 259 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: Q 307 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.5827 (mtt) REVERT: Q 344 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8886 (mptm) REVERT: Q 353 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.4865 (tmm-80) REVERT: R 196 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: R 259 GLU cc_start: 0.8145 (tp30) cc_final: 0.7891 (tp30) REVERT: R 260 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8020 (ttpp) REVERT: R 337 PHE cc_start: 0.5782 (OUTLIER) cc_final: 0.4007 (t80) REVERT: S 181 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: F 296 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8056 (tt0) REVERT: F 300 SER cc_start: 0.8872 (p) cc_final: 0.8574 (p) REVERT: F 301 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8233 (mt-10) REVERT: F 319 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7510 (mp) REVERT: H 301 GLU cc_start: 0.8966 (pm20) cc_final: 0.8569 (pt0) REVERT: H 307 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: J 307 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8419 (tt0) outliers start: 160 outliers final: 68 residues processed: 485 average time/residue: 0.6796 time to fit residues: 395.5074 Evaluate side-chains 451 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 365 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 121 MET Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 167 ARG Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 133 ASP Chi-restraints excluded: chain O residue 303 SER Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain Q residue 344 LYS Chi-restraints excluded: chain Q residue 353 ARG Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 196 PHE Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 340 LEU Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain S residue 340 LEU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 307 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 143 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 406 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 363 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 chunk 318 optimal weight: 7.9990 chunk 408 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 253 GLN K 183 ASN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN Q 212 ASN R 115 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085586 restraints weight = 57226.961| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.25 r_work: 0.3022 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 33626 Z= 0.241 Angle : 0.560 11.799 45775 Z= 0.293 Chirality : 0.046 0.196 5176 Planarity : 0.004 0.047 6008 Dihedral : 5.262 57.687 4667 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.07 % Allowed : 22.68 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4287 helix: 1.55 (0.16), residues: 1008 sheet: 0.15 (0.15), residues: 1052 loop : -0.88 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 25 TYR 0.019 0.002 TYR E 131 PHE 0.014 0.002 PHE E 196 TRP 0.010 0.001 TRP N 86 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00575 (33626) covalent geometry : angle 0.55996 (45775) hydrogen bonds : bond 0.03902 ( 1182) hydrogen bonds : angle 5.34648 ( 3243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 366 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 255 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7468 (t0) REVERT: B 172 ARG cc_start: 0.8390 (mpp-170) cc_final: 0.7986 (mpp-170) REVERT: B 288 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8832 (tp30) REVERT: B 351 GLU cc_start: 0.4914 (OUTLIER) cc_final: 0.4503 (tp30) REVERT: C 95 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7557 (p) REVERT: C 109 VAL cc_start: 0.8903 (p) cc_final: 0.8612 (m) REVERT: C 303 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9149 (p) REVERT: C 310 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: D 351 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5428 (mm-30) REVERT: E 310 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: K 141 TYR cc_start: 0.8443 (t80) cc_final: 0.8095 (t80) REVERT: K 211 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: M 174 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8810 (tpp) REVERT: N 167 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8475 (mmt180) REVERT: O 260 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8906 (mtmm) REVERT: P 147 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8370 (mm-30) REVERT: P 311 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: Q 106 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8577 (tp) REVERT: Q 344 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9029 (mptm) REVERT: R 181 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: R 259 GLU cc_start: 0.8216 (tp30) cc_final: 0.7932 (tp30) REVERT: R 260 LYS cc_start: 0.8646 (mtpp) cc_final: 0.7955 (ttpp) REVERT: R 288 GLU cc_start: 0.8605 (pt0) cc_final: 0.8346 (pt0) REVERT: R 337 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.3700 (t80) REVERT: S 158 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8505 (ptp) REVERT: S 181 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: F 296 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8222 (tt0) REVERT: F 300 SER cc_start: 0.9155 (p) cc_final: 0.8818 (p) REVERT: F 301 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8367 (mt-10) REVERT: F 319 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7497 (mp) REVERT: H 301 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8735 (pt0) REVERT: H 307 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: J 307 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8326 (tt0) outliers start: 176 outliers final: 86 residues processed: 491 average time/residue: 0.7075 time to fit residues: 415.6093 Evaluate side-chains 476 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 367 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 211 GLN Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 174 MET Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 167 ARG Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 133 ASP Chi-restraints excluded: chain O residue 135 THR Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 297 VAL Chi-restraints excluded: chain O residue 303 SER Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 311 GLU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 316 LEU Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain Q residue 344 LYS Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 268 SER Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 340 LEU Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 158 MET Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain S residue 331 THR Chi-restraints excluded: chain S residue 340 LEU Chi-restraints excluded: chain S residue 344 LYS Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain H residue 301 GLU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 307 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 108 optimal weight: 0.0020 chunk 315 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 410 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 417 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 ASN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088188 restraints weight = 56786.856| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.26 r_work: 0.3072 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33626 Z= 0.111 Angle : 0.480 9.778 45775 Z= 0.252 Chirality : 0.043 0.192 5176 Planarity : 0.003 0.047 6008 Dihedral : 4.835 58.570 4658 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.38 % Allowed : 23.89 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 4287 helix: 1.80 (0.16), residues: 1004 sheet: 0.16 (0.16), residues: 1057 loop : -0.80 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 206 TYR 0.016 0.001 TYR S 197 PHE 0.011 0.001 PHE L 169 TRP 0.010 0.001 TRP N 232 HIS 0.002 0.000 HIS M 93 Details of bonding type rmsd covalent geometry : bond 0.00261 (33626) covalent geometry : angle 0.48032 (45775) hydrogen bonds : bond 0.03183 ( 1182) hydrogen bonds : angle 5.05098 ( 3243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 383 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8230 (pp) REVERT: B 109 VAL cc_start: 0.9001 (m) cc_final: 0.8751 (p) REVERT: B 172 ARG cc_start: 0.8350 (mpp-170) cc_final: 0.7956 (mpp-170) REVERT: B 288 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8870 (tp30) REVERT: B 351 GLU cc_start: 0.4844 (OUTLIER) cc_final: 0.4613 (tp30) REVERT: B 355 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8893 (ptmt) REVERT: C 95 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7299 (p) REVERT: C 109 VAL cc_start: 0.8894 (p) cc_final: 0.8601 (m) REVERT: C 255 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7390 (t0) REVERT: C 310 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: D 196 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.9234 (m-80) REVERT: D 267 THR cc_start: 0.9342 (t) cc_final: 0.8904 (m) REVERT: D 351 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5172 (mm-30) REVERT: E 310 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: E 351 GLU cc_start: 0.4817 (OUTLIER) cc_final: 0.3046 (tp30) REVERT: K 141 TYR cc_start: 0.8393 (t80) cc_final: 0.8083 (t80) REVERT: K 185 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8720 (mtm110) REVERT: L 102 ASP cc_start: 0.8153 (t0) cc_final: 0.7901 (t0) REVERT: M 174 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8773 (tpp) REVERT: N 167 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7953 (mmt-90) REVERT: P 147 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8525 (mm-30) REVERT: P 289 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: P 311 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: Q 259 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: Q 353 ARG cc_start: 0.6611 (tmm-80) cc_final: 0.5165 (tmm-80) REVERT: R 181 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8070 (mm110) REVERT: R 196 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: R 259 GLU cc_start: 0.8096 (tp30) cc_final: 0.7863 (tp30) REVERT: R 260 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8004 (ttpp) REVERT: R 288 GLU cc_start: 0.8558 (pt0) cc_final: 0.8309 (pt0) REVERT: R 295 ARG cc_start: 0.8937 (ttp80) cc_final: 0.8722 (ttp80) REVERT: R 337 PHE cc_start: 0.5712 (OUTLIER) cc_final: 0.3777 (t80) REVERT: S 159 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.5767 (mpt) REVERT: S 181 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: F 300 SER cc_start: 0.9170 (p) cc_final: 0.8834 (p) REVERT: F 319 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7435 (mp) REVERT: H 301 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8750 (pt0) REVERT: H 307 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8309 (tt0) outliers start: 152 outliers final: 73 residues processed: 495 average time/residue: 0.7244 time to fit residues: 427.5530 Evaluate side-chains 467 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 369 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 174 MET Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 167 ARG Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 133 ASP Chi-restraints excluded: chain O residue 297 VAL Chi-restraints excluded: chain O residue 303 SER Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 311 GLU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 259 GLU Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 196 PHE Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 268 SER Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain S residue 340 LEU Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain H residue 301 GLU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 287 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 335 optimal weight: 0.2980 chunk 216 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 396 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN ** N 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN O 339 GLN Q 212 ASN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086020 restraints weight = 57780.587| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.29 r_work: 0.3028 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33626 Z= 0.209 Angle : 0.534 10.715 45775 Z= 0.279 Chirality : 0.045 0.190 5176 Planarity : 0.004 0.047 6008 Dihedral : 4.923 58.035 4654 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.87 % Allowed : 23.66 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4287 helix: 1.63 (0.16), residues: 1011 sheet: 0.15 (0.16), residues: 1052 loop : -0.85 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 206 TYR 0.017 0.002 TYR E 131 PHE 0.011 0.002 PHE P 319 TRP 0.009 0.001 TRP S 232 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00503 (33626) covalent geometry : angle 0.53448 (45775) hydrogen bonds : bond 0.03613 ( 1182) hydrogen bonds : angle 5.19102 ( 3243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 375 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 255 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7650 (t0) REVERT: B 83 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8534 (pp) REVERT: B 172 ARG cc_start: 0.8380 (mpp-170) cc_final: 0.7980 (mpp-170) REVERT: B 288 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8873 (tp30) REVERT: B 313 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: B 324 ASN cc_start: 0.8959 (p0) cc_final: 0.8729 (p0) REVERT: B 351 GLU cc_start: 0.4823 (OUTLIER) cc_final: 0.4366 (tp30) REVERT: B 355 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8942 (ptmt) REVERT: C 95 THR cc_start: 0.8032 (m) cc_final: 0.7593 (p) REVERT: C 109 VAL cc_start: 0.8933 (p) cc_final: 0.8644 (m) REVERT: C 255 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7441 (t0) REVERT: C 310 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: C 351 GLU cc_start: 0.5260 (mm-30) cc_final: 0.4958 (mm-30) REVERT: D 351 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.4948 (mm-30) REVERT: D 353 ARG cc_start: 0.8952 (mtt180) cc_final: 0.8732 (mtt180) REVERT: E 310 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: E 351 GLU cc_start: 0.5111 (OUTLIER) cc_final: 0.3111 (tp30) REVERT: K 141 TYR cc_start: 0.8376 (t80) cc_final: 0.8075 (t80) REVERT: K 211 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: M 174 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8710 (tpp) REVERT: N 167 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8204 (mmt180) REVERT: N 179 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9141 (mttp) REVERT: O 260 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8887 (mtmm) REVERT: P 311 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: Q 158 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8773 (ptm) REVERT: Q 307 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5851 (mtt) REVERT: Q 344 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8854 (mptm) REVERT: Q 353 ARG cc_start: 0.6632 (tmm-80) cc_final: 0.5146 (tmm-80) REVERT: R 92 LYS cc_start: 0.8333 (ptpp) cc_final: 0.8018 (ptpp) REVERT: R 133 ASP cc_start: 0.2828 (OUTLIER) cc_final: 0.1383 (m-30) REVERT: R 181 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: R 259 GLU cc_start: 0.8218 (tp30) cc_final: 0.7940 (tp30) REVERT: R 260 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8009 (ttpp) REVERT: R 288 GLU cc_start: 0.8590 (pt0) cc_final: 0.8339 (pt0) REVERT: R 295 ARG cc_start: 0.8941 (ttp80) cc_final: 0.8733 (ttp80) REVERT: R 337 PHE cc_start: 0.5837 (OUTLIER) cc_final: 0.4009 (t80) REVERT: S 181 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: F 300 SER cc_start: 0.9293 (p) cc_final: 0.8993 (p) REVERT: F 319 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7559 (mp) REVERT: H 301 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8874 (pt0) REVERT: H 307 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: J 296 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7457 (mm-30) REVERT: J 307 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8197 (tt0) outliers start: 169 outliers final: 94 residues processed: 497 average time/residue: 0.6814 time to fit residues: 405.9926 Evaluate side-chains 491 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 368 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 129 ILE Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 211 GLN Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 174 MET Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 167 ARG Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 133 ASP Chi-restraints excluded: chain O residue 135 THR Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 297 VAL Chi-restraints excluded: chain O residue 303 SER Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 311 GLU Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain Q residue 316 LEU Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain Q residue 344 LYS Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 268 SER Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 340 LEU Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain S residue 331 THR Chi-restraints excluded: chain S residue 340 LEU Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain H residue 301 GLU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 307 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 366 optimal weight: 0.0010 chunk 347 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 405 optimal weight: 3.9990 chunk 412 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 ASN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087773 restraints weight = 57132.287| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.27 r_work: 0.3064 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33626 Z= 0.119 Angle : 0.490 9.415 45775 Z= 0.256 Chirality : 0.043 0.181 5176 Planarity : 0.003 0.045 6008 Dihedral : 4.771 58.592 4653 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.35 % Allowed : 24.52 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 4287 helix: 1.83 (0.16), residues: 1003 sheet: 0.14 (0.16), residues: 1057 loop : -0.81 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 206 TYR 0.016 0.001 TYR B 279 PHE 0.011 0.001 PHE K 118 TRP 0.010 0.001 TRP N 232 HIS 0.002 0.000 HIS M 93 Details of bonding type rmsd covalent geometry : bond 0.00282 (33626) covalent geometry : angle 0.48960 (45775) hydrogen bonds : bond 0.03196 ( 1182) hydrogen bonds : angle 5.02520 ( 3243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 380 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8569 (pp) REVERT: A 255 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7528 (t0) REVERT: B 83 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8323 (pp) REVERT: B 172 ARG cc_start: 0.8353 (mpp-170) cc_final: 0.7984 (mpp-170) REVERT: B 288 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8919 (tp30) REVERT: B 324 ASN cc_start: 0.8934 (p0) cc_final: 0.8686 (p0) REVERT: B 351 GLU cc_start: 0.4357 (OUTLIER) cc_final: 0.4022 (tp30) REVERT: B 355 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8890 (ptmt) REVERT: C 95 THR cc_start: 0.7926 (m) cc_final: 0.7502 (p) REVERT: C 109 VAL cc_start: 0.8933 (p) cc_final: 0.8666 (m) REVERT: C 310 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6826 (tm-30) REVERT: D 196 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.9230 (m-80) REVERT: D 267 THR cc_start: 0.9338 (t) cc_final: 0.8899 (m) REVERT: D 351 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.5214 (mm-30) REVERT: E 310 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: E 351 GLU cc_start: 0.4891 (OUTLIER) cc_final: 0.3096 (tp30) REVERT: K 141 TYR cc_start: 0.8307 (t80) cc_final: 0.8083 (t80) REVERT: K 185 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8730 (mtm110) REVERT: M 174 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8693 (tpp) REVERT: N 167 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7943 (mmt-90) REVERT: O 101 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: O 196 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.7355 (t80) REVERT: O 260 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8870 (mtmm) REVERT: P 311 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: Q 107 ASP cc_start: 0.7099 (m-30) cc_final: 0.6870 (m-30) REVERT: Q 158 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8709 (ptm) REVERT: Q 344 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8874 (mptm) REVERT: Q 353 ARG cc_start: 0.6543 (tmm-80) cc_final: 0.5055 (tmm-80) REVERT: R 92 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7944 (ptpp) REVERT: R 181 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: R 259 GLU cc_start: 0.8161 (tp30) cc_final: 0.7932 (tp30) REVERT: R 260 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8076 (ttpp) REVERT: R 288 GLU cc_start: 0.8557 (pt0) cc_final: 0.8304 (pt0) REVERT: R 337 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.3965 (t80) REVERT: S 181 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: F 319 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7442 (mp) REVERT: H 301 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8837 (pt0) REVERT: H 307 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: J 296 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: J 307 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8130 (tt0) outliers start: 151 outliers final: 85 residues processed: 486 average time/residue: 0.7207 time to fit residues: 418.4983 Evaluate side-chains 482 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 369 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 174 MET Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 167 ARG Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 133 ASP Chi-restraints excluded: chain O residue 196 PHE Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 297 VAL Chi-restraints excluded: chain O residue 303 SER Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 311 GLU Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 260 LYS Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 316 LEU Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain Q residue 344 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 340 LEU Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain S residue 331 THR Chi-restraints excluded: chain S residue 340 LEU Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain H residue 301 GLU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 307 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 157 optimal weight: 0.9980 chunk 315 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 94 optimal weight: 0.0000 chunk 194 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN K 183 ASN M 183 ASN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 GLN O 136 ASN Q 212 ASN R 115 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.089195 restraints weight = 57503.757| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.29 r_work: 0.3083 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33626 Z= 0.100 Angle : 0.477 9.899 45775 Z= 0.249 Chirality : 0.043 0.174 5176 Planarity : 0.003 0.045 6008 Dihedral : 4.648 58.571 4653 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.12 % Allowed : 24.78 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4287 helix: 2.01 (0.17), residues: 995 sheet: 0.34 (0.17), residues: 961 loop : -0.75 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 206 TYR 0.018 0.001 TYR D 279 PHE 0.010 0.001 PHE L 169 TRP 0.011 0.001 TRP N 232 HIS 0.002 0.000 HIS M 93 Details of bonding type rmsd covalent geometry : bond 0.00237 (33626) covalent geometry : angle 0.47701 (45775) hydrogen bonds : bond 0.02984 ( 1182) hydrogen bonds : angle 4.88860 ( 3243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 383 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8543 (pp) REVERT: A 353 ARG cc_start: 0.8657 (mtt90) cc_final: 0.7201 (tpm170) REVERT: B 83 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8285 (pp) REVERT: B 109 VAL cc_start: 0.8933 (m) cc_final: 0.8658 (p) REVERT: B 172 ARG cc_start: 0.8335 (mpp-170) cc_final: 0.7960 (mpp-170) REVERT: B 324 ASN cc_start: 0.8951 (p0) cc_final: 0.8690 (p0) REVERT: B 351 GLU cc_start: 0.4308 (OUTLIER) cc_final: 0.4042 (tp30) REVERT: B 365 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9024 (t) REVERT: C 95 THR cc_start: 0.7912 (m) cc_final: 0.7525 (p) REVERT: C 109 VAL cc_start: 0.8916 (p) cc_final: 0.8636 (m) REVERT: C 310 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: D 267 THR cc_start: 0.9329 (t) cc_final: 0.9121 (m) REVERT: D 351 GLU cc_start: 0.5410 (mm-30) cc_final: 0.5111 (mm-30) REVERT: D 353 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8719 (mtt180) REVERT: E 285 ASP cc_start: 0.8895 (t0) cc_final: 0.8574 (t0) REVERT: E 310 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: E 351 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.3442 (tp30) REVERT: K 185 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8744 (mtm110) REVERT: M 174 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8680 (tpp) REVERT: O 101 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: O 196 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.7299 (t80) REVERT: O 260 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8892 (mtmm) REVERT: P 289 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: P 311 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: Q 107 ASP cc_start: 0.7306 (m-30) cc_final: 0.7090 (m-30) REVERT: Q 158 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8735 (ptm) REVERT: Q 353 ARG cc_start: 0.6549 (tmm-80) cc_final: 0.6257 (tmt90) REVERT: R 181 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: R 260 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8044 (ttpp) REVERT: R 288 GLU cc_start: 0.8514 (pt0) cc_final: 0.8265 (pt0) REVERT: R 337 PHE cc_start: 0.5902 (OUTLIER) cc_final: 0.4055 (t80) REVERT: S 159 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.5782 (mpt) REVERT: S 181 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: F 319 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7507 (mp) REVERT: H 301 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8769 (pt0) REVERT: I 295 GLN cc_start: 0.7599 (mm110) cc_final: 0.6604 (mt0) REVERT: J 296 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: J 307 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8127 (tt0) outliers start: 143 outliers final: 77 residues processed: 483 average time/residue: 0.7221 time to fit residues: 416.5105 Evaluate side-chains 468 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 368 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 129 ILE Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 174 MET Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 196 PHE Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 297 VAL Chi-restraints excluded: chain O residue 303 SER Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 311 GLU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 316 LEU Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 340 LEU Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain R residue 371 LYS Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 331 THR Chi-restraints excluded: chain S residue 340 LEU Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain H residue 301 GLU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 307 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 263 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 364 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 409 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN L 47 ASN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN Q 212 ASN Q 306 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084958 restraints weight = 57160.102| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.29 r_work: 0.3038 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33626 Z= 0.177 Angle : 0.534 12.513 45775 Z= 0.277 Chirality : 0.044 0.181 5176 Planarity : 0.004 0.044 6008 Dihedral : 4.781 58.081 4651 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.86 % Allowed : 25.04 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 4287 helix: 1.79 (0.16), residues: 1003 sheet: 0.06 (0.15), residues: 1115 loop : -0.74 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 295 TYR 0.019 0.002 TYR B 197 PHE 0.011 0.001 PHE K 118 TRP 0.008 0.001 TRP N 86 HIS 0.002 0.001 HIS N 134 Details of bonding type rmsd covalent geometry : bond 0.00421 (33626) covalent geometry : angle 0.53360 (45775) hydrogen bonds : bond 0.03438 ( 1182) hydrogen bonds : angle 5.05706 ( 3243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 370 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8592 (pp) REVERT: B 83 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8398 (pp) REVERT: B 172 ARG cc_start: 0.8366 (mpp-170) cc_final: 0.7973 (mpp-170) REVERT: B 324 ASN cc_start: 0.8943 (p0) cc_final: 0.8691 (p0) REVERT: B 351 GLU cc_start: 0.4539 (OUTLIER) cc_final: 0.4287 (tp30) REVERT: B 365 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9029 (t) REVERT: C 95 THR cc_start: 0.7941 (m) cc_final: 0.7531 (p) REVERT: C 109 VAL cc_start: 0.8954 (p) cc_final: 0.8673 (m) REVERT: C 303 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8968 (p) REVERT: C 310 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: C 351 GLU cc_start: 0.5338 (mm-30) cc_final: 0.4922 (mt-10) REVERT: D 267 THR cc_start: 0.9373 (t) cc_final: 0.8929 (m) REVERT: D 351 GLU cc_start: 0.5384 (OUTLIER) cc_final: 0.4928 (mm-30) REVERT: D 353 ARG cc_start: 0.8966 (mtt180) cc_final: 0.8723 (mtt180) REVERT: E 83 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8483 (pp) REVERT: E 94 MET cc_start: 0.8341 (tpp) cc_final: 0.8136 (mmt) REVERT: E 285 ASP cc_start: 0.8923 (t0) cc_final: 0.8615 (t0) REVERT: E 310 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: M 174 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8923 (ttp) REVERT: N 167 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8005 (mmt-90) REVERT: O 196 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.7281 (t80) REVERT: O 260 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8879 (mtmm) REVERT: P 289 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: P 311 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: Q 158 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8705 (ptm) REVERT: Q 353 ARG cc_start: 0.6560 (tmm-80) cc_final: 0.6263 (tmt90) REVERT: R 133 ASP cc_start: 0.3139 (OUTLIER) cc_final: 0.1379 (m-30) REVERT: R 181 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: R 196 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: R 259 GLU cc_start: 0.8091 (tp30) cc_final: 0.7769 (tp30) REVERT: R 260 LYS cc_start: 0.8600 (mtpp) cc_final: 0.7524 (ttpp) REVERT: R 288 GLU cc_start: 0.8572 (pt0) cc_final: 0.8328 (pt0) REVERT: R 337 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.4063 (t80) REVERT: S 181 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8050 (mp10) REVERT: F 319 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7522 (mp) REVERT: I 295 GLN cc_start: 0.7682 (mm110) cc_final: 0.6631 (mt0) REVERT: J 296 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: J 307 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8161 (tt0) outliers start: 134 outliers final: 85 residues processed: 467 average time/residue: 0.7206 time to fit residues: 402.7520 Evaluate side-chains 478 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 369 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 129 ILE Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 174 MET Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 167 ARG Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 133 ASP Chi-restraints excluded: chain O residue 196 PHE Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 297 VAL Chi-restraints excluded: chain O residue 303 SER Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 311 GLU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 260 LYS Chi-restraints excluded: chain Q residue 316 LEU Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 196 PHE Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 340 LEU Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain R residue 371 LYS Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 331 THR Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 307 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 171 optimal weight: 0.9990 chunk 345 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 354 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 333 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 ASN Q 306 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087961 restraints weight = 57979.837| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.30 r_work: 0.3067 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33626 Z= 0.115 Angle : 0.505 13.349 45775 Z= 0.262 Chirality : 0.043 0.178 5176 Planarity : 0.004 0.050 6008 Dihedral : 4.706 58.584 4651 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.37 % Allowed : 25.48 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4287 helix: 1.86 (0.16), residues: 1003 sheet: 0.14 (0.16), residues: 1082 loop : -0.73 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 206 TYR 0.018 0.001 TYR K 141 PHE 0.010 0.001 PHE L 169 TRP 0.009 0.001 TRP N 232 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00272 (33626) covalent geometry : angle 0.50459 (45775) hydrogen bonds : bond 0.03139 ( 1182) hydrogen bonds : angle 4.94304 ( 3243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 372 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8543 (pp) REVERT: B 83 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8323 (pp) REVERT: B 109 VAL cc_start: 0.8966 (m) cc_final: 0.8691 (p) REVERT: B 172 ARG cc_start: 0.8345 (mpp-170) cc_final: 0.7952 (mpp-170) REVERT: B 324 ASN cc_start: 0.8930 (p0) cc_final: 0.8686 (p0) REVERT: B 351 GLU cc_start: 0.4431 (OUTLIER) cc_final: 0.4174 (tp30) REVERT: B 365 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9014 (t) REVERT: C 95 THR cc_start: 0.7806 (m) cc_final: 0.7437 (p) REVERT: C 109 VAL cc_start: 0.8937 (p) cc_final: 0.8661 (m) REVERT: C 310 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: C 351 GLU cc_start: 0.5254 (mm-30) cc_final: 0.4853 (mt-10) REVERT: D 267 THR cc_start: 0.9339 (t) cc_final: 0.9126 (m) REVERT: D 351 GLU cc_start: 0.5211 (mm-30) cc_final: 0.4806 (mm-30) REVERT: D 353 ARG cc_start: 0.8959 (mtt180) cc_final: 0.8735 (mtt180) REVERT: D 365 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.8940 (t) REVERT: E 95 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8492 (t) REVERT: E 310 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: E 351 GLU cc_start: 0.4877 (OUTLIER) cc_final: 0.3157 (tp30) REVERT: K 75 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8894 (t) REVERT: M 174 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8915 (ttp) REVERT: N 167 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7995 (mmt-90) REVERT: O 196 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.7364 (t80) REVERT: O 260 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8877 (mtmm) REVERT: P 289 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: P 311 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: Q 158 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8728 (ptm) REVERT: Q 353 ARG cc_start: 0.6474 (tmm-80) cc_final: 0.6158 (tmt90) REVERT: R 92 LYS cc_start: 0.8358 (ptpp) cc_final: 0.7899 (ptpp) REVERT: R 133 ASP cc_start: 0.3387 (OUTLIER) cc_final: 0.1605 (m-30) REVERT: R 181 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: R 196 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: R 260 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8001 (ttpp) REVERT: R 288 GLU cc_start: 0.8540 (pt0) cc_final: 0.8291 (pt0) REVERT: R 337 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.4048 (t80) REVERT: S 181 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: F 319 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7516 (mp) REVERT: I 295 GLN cc_start: 0.7689 (mm110) cc_final: 0.6629 (mt0) REVERT: J 296 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7440 (mm-30) REVERT: J 307 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8125 (tt0) outliers start: 117 outliers final: 79 residues processed: 467 average time/residue: 0.6923 time to fit residues: 386.5661 Evaluate side-chains 470 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 366 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 108 TYR Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 174 MET Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 167 ARG Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 133 ASP Chi-restraints excluded: chain O residue 196 PHE Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 297 VAL Chi-restraints excluded: chain O residue 303 SER Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 311 GLU Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 148 ARG Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 196 PHE Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 340 LEU Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain R residue 371 LYS Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 331 THR Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 307 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 342 optimal weight: 7.9990 chunk 337 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 260 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN B 253 GLN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN Q 212 ASN Q 306 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 GLN H 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087701 restraints weight = 56983.361| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.29 r_work: 0.3088 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33626 Z= 0.101 Angle : 0.490 13.260 45775 Z= 0.254 Chirality : 0.043 0.175 5176 Planarity : 0.003 0.049 6008 Dihedral : 4.600 59.354 4651 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.43 % Allowed : 25.48 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.13), residues: 4287 helix: 1.98 (0.17), residues: 1003 sheet: 0.19 (0.16), residues: 1057 loop : -0.74 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 206 TYR 0.018 0.001 TYR B 197 PHE 0.012 0.001 PHE M 2 TRP 0.011 0.001 TRP N 232 HIS 0.002 0.000 HIS M 93 Details of bonding type rmsd covalent geometry : bond 0.00238 (33626) covalent geometry : angle 0.48990 (45775) hydrogen bonds : bond 0.02932 ( 1182) hydrogen bonds : angle 4.81790 ( 3243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13847.11 seconds wall clock time: 235 minutes 47.70 seconds (14147.70 seconds total)