Starting phenix.real_space_refine on Thu May 29 23:37:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b40_44163/05_2025/9b40_44163.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b40_44163/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b40_44163/05_2025/9b40_44163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b40_44163/05_2025/9b40_44163.map" model { file = "/net/cci-nas-00/data/ceres_data/9b40_44163/05_2025/9b40_44163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b40_44163/05_2025/9b40_44163.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.88, per 1000 atoms: 0.57 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: 7.64 Conformation dependent library (CDL) restraints added in 4.2 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: 4.01 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: 11.86 Time building geometry restraints manager: 9.01 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: 0.02 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.230 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 69.180 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.240 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:13.810 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.710 ------------------------------------------------------------------------------- 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 : 3.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (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 TRP 0.014 0.001 TRP R 227 HIS 0.003 0.001 HIS L 93 PHE 0.019 0.002 PHE L 169 TYR 0.031 0.002 TYR Q 131 ARG 0.015 0.001 ARG R 295 Details of bonding type rmsd hydrogen bonds : bond 0.13941 ( 1182) hydrogen bonds : angle 6.79568 ( 3243) covalent geometry : bond 0.00438 (33626) covalent geometry : angle 0.71996 (45775) *********************** 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 : 3.639 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: 0.8785 (ttm170) REVERT: K 76 GLU cc_start: 0.8431 (tt0) cc_final: 0.8222 (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: 0.8548 (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: 0.8382 (ptm) REVERT: H 301 GLU cc_start: 0.8922 (pm20) cc_final: 0.8441 (pt0) outliers start: 133 outliers final: 70 residues processed: 515 average time/residue: 1.3632 time to fit residues: 842.7842 Evaluate side-chains 448 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 374 time to evaluate : 3.525 ------------------------------------------------------------------------------- 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 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 358 optimal weight: 0.9980 chunk 321 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 171 optimal weight: 0.9980 chunk 332 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 385 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 47 ASN L 183 ASN L 208 GLN N 181 GLN O 136 ASN ** O 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 ASN Q 306 GLN R 115 GLN R 143 ASN 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 = 0.3443 r_free = 0.3443 target = 0.103400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.085287 restraints weight = 57424.587| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.26 r_work: 0.3017 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 33626 Z= 0.273 Angle : 0.604 14.050 45775 Z= 0.316 Chirality : 0.047 0.169 5176 Planarity : 0.005 0.050 6008 Dihedral : 6.482 58.003 4755 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.30 % Allowed : 21.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 4287 helix: 1.28 (0.16), residues: 1007 sheet: 0.03 (0.15), residues: 1083 loop : -0.99 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 86 HIS 0.004 0.001 HIS L 90 PHE 0.015 0.002 PHE A 337 TYR 0.018 0.002 TYR B 131 ARG 0.008 0.001 ARG R 295 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 1182) hydrogen bonds : angle 5.66020 ( 3243) covalent geometry : bond 0.00653 (33626) covalent geometry : angle 0.60384 (45775) *********************** 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 575 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 391 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8495 (t80) REVERT: B 172 ARG cc_start: 0.8429 (mpp-170) cc_final: 0.8110 (mpp-170) REVERT: B 197 TYR cc_start: 0.9087 (m-80) cc_final: 0.8838 (m-80) REVERT: B 288 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8827 (tp30) REVERT: B 303 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 324 ASN cc_start: 0.8951 (p0) cc_final: 0.8702 (p0) REVERT: B 351 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.4907 (tp30) REVERT: C 109 VAL cc_start: 0.8826 (p) cc_final: 0.8541 (m) REVERT: D 165 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: D 267 THR cc_start: 0.9573 (t) cc_final: 0.9344 (t) REVERT: D 351 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5305 (mm-30) REVERT: D 353 ARG cc_start: 0.8947 (mtt180) cc_final: 0.8731 (mtt180) REVERT: E 165 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: E 219 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8392 (t80) REVERT: E 285 ASP cc_start: 0.8825 (t0) cc_final: 0.8623 (t0) REVERT: K 173 SER cc_start: 0.8766 (m) cc_final: 0.8499 (m) REVERT: M 195 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8777 (pt0) REVERT: N 167 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8199 (mmt180) REVERT: O 260 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8903 (mtmm) REVERT: P 102 GLU cc_start: 0.8314 (mp0) cc_final: 0.8061 (mp0) REVERT: Q 106 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8414 (tp) REVERT: R 259 GLU cc_start: 0.8308 (tp30) cc_final: 0.7977 (tp30) REVERT: R 260 LYS cc_start: 0.8646 (mtpp) cc_final: 0.7938 (ttpp) REVERT: R 306 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8612 (mt0) REVERT: R 337 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5601 (t80) REVERT: S 158 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8432 (ptp) REVERT: S 181 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: F 296 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7989 (tt0) REVERT: F 301 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8326 (mt-10) REVERT: F 319 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7588 (mp) REVERT: H 301 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8745 (pt0) REVERT: J 301 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: J 307 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8302 (tt0) outliers start: 184 outliers final: 82 residues processed: 517 average time/residue: 1.3619 time to fit residues: 851.0525 Evaluate side-chains 473 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 371 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 94 MET 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 271 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 282 SER 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 143 ASN 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 331 THR 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 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 44 THR Chi-restraints excluded: chain L residue 108 TYR Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain M residue 108 TYR 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 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 236 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 133 ASP Chi-restraints excluded: chain O residue 135 THR Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 277 THR 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 158 MET Chi-restraints excluded: chain P residue 294 MET Chi-restraints excluded: chain P residue 382 ILE 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 254 ILE Chi-restraints excluded: chain Q residue 260 LYS Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 306 GLN 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 73 THR Chi-restraints excluded: chain S residue 94 MET 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 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 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 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 336 optimal weight: 0.6980 chunk 329 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 233 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN C 253 GLN K 5 GLN K 183 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.104977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086998 restraints weight = 57471.390| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.28 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: 0.8629 moved from start: 0.1192 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= 0.109 Angle : 0.484 10.939 45775 Z= 0.255 Chirality : 0.043 0.198 5176 Planarity : 0.004 0.047 6008 Dihedral : 5.155 59.418 4678 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.52 % Allowed : 23.14 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 4287 helix: 1.72 (0.16), residues: 1003 sheet: 0.14 (0.15), residues: 1075 loop : -0.85 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 232 HIS 0.002 0.000 HIS M 93 PHE 0.012 0.001 PHE L 169 TYR 0.015 0.001 TYR S 197 ARG 0.007 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 1182) hydrogen bonds : angle 5.21220 ( 3243) covalent geometry : bond 0.00253 (33626) covalent geometry : angle 0.48378 (45775) *********************** 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 541 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 384 time to evaluate : 3.794 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8551 (t0) REVERT: A 219 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8514 (t80) REVERT: B 109 VAL cc_start: 0.9053 (m) cc_final: 0.8806 (p) REVERT: B 172 ARG cc_start: 0.8363 (mpp-170) cc_final: 0.7978 (mpp-170) REVERT: B 197 TYR cc_start: 0.9091 (m-80) cc_final: 0.8873 (m-80) REVERT: B 288 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8847 (tp30) REVERT: B 324 ASN cc_start: 0.8937 (p0) cc_final: 0.8671 (p0) REVERT: B 351 GLU cc_start: 0.4883 (OUTLIER) cc_final: 0.4642 (tp30) REVERT: C 98 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8896 (mtm180) REVERT: C 109 VAL cc_start: 0.8807 (p) cc_final: 0.8491 (m) REVERT: C 303 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8830 (p) REVERT: C 310 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: D 267 THR cc_start: 0.9562 (t) cc_final: 0.9012 (m) REVERT: E 219 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8412 (t80) REVERT: E 351 GLU cc_start: 0.4787 (OUTLIER) cc_final: 0.3184 (tp30) REVERT: K 1 MET cc_start: 0.7836 (tpp) cc_final: 0.7604 (tpp) REVERT: K 141 TYR cc_start: 0.8323 (t80) cc_final: 0.7960 (t80) REVERT: O 371 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8334 (mtpt) REVERT: Q 307 MET cc_start: 0.6071 (OUTLIER) cc_final: 0.5818 (mtt) REVERT: R 196 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8072 (m-80) REVERT: R 259 GLU cc_start: 0.8101 (tp30) cc_final: 0.7790 (tp30) REVERT: R 260 LYS cc_start: 0.8645 (mtpp) cc_final: 0.7899 (ttpp) REVERT: S 177 GLU cc_start: 0.8517 (tp30) cc_final: 0.7867 (tp30) REVERT: S 181 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: F 296 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8135 (tt0) REVERT: F 301 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8320 (mt-10) REVERT: F 319 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7490 (mp) REVERT: H 301 GLU cc_start: 0.8962 (pm20) cc_final: 0.8617 (pt0) REVERT: H 307 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: J 307 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8394 (tt0) outliers start: 157 outliers final: 63 residues processed: 494 average time/residue: 1.3888 time to fit residues: 822.6521 Evaluate side-chains 452 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 373 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 ASP 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 346 ILE 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 B residue 351 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 310 GLN 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 121 ILE 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 49 ILE Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 108 TYR 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 1 MET 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 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 135 THR 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 O residue 371 LYS 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 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 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 268 SER Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 347 THR Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 298 SER 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 Chi-restraints excluded: chain J residue 308 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 108 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 415 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 81 GLN B 253 GLN L 131 ASN L 183 ASN M 183 ASN N 212 ASN ** N 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN O 339 GLN O 342 GLN O 363 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** H 314 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.081637 restraints weight = 57930.346| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.27 r_work: 0.2979 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 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 : 0.009 0.080 33626 Z= 0.356 Angle : 0.650 12.503 45775 Z= 0.339 Chirality : 0.049 0.194 5176 Planarity : 0.005 0.049 6008 Dihedral : 5.418 57.337 4659 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.79 % Allowed : 22.65 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 4287 helix: 1.25 (0.16), residues: 1005 sheet: -0.12 (0.15), residues: 1110 loop : -0.94 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 86 HIS 0.003 0.001 HIS S 134 PHE 0.017 0.002 PHE E 337 TYR 0.022 0.002 TYR E 131 ARG 0.009 0.001 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.04468 ( 1182) hydrogen bonds : angle 5.57411 ( 3243) covalent geometry : bond 0.00854 (33626) covalent geometry : angle 0.65041 (45775) *********************** 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 563 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 362 time to evaluate : 3.585 Fit side-chains REVERT: A 101 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8572 (t0) REVERT: A 255 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7711 (t0) REVERT: B 83 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8543 (pp) REVERT: B 143 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8928 (p0) REVERT: B 167 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8544 (mmt180) REVERT: B 172 ARG cc_start: 0.8390 (mpp-170) cc_final: 0.7985 (mpp-170) REVERT: B 351 GLU cc_start: 0.5252 (OUTLIER) cc_final: 0.4619 (tp30) REVERT: C 95 THR cc_start: 0.8290 (m) cc_final: 0.8004 (p) REVERT: C 310 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: C 351 GLU cc_start: 0.5330 (OUTLIER) cc_final: 0.4675 (mm-30) REVERT: D 165 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: D 267 THR cc_start: 0.9576 (t) cc_final: 0.9346 (t) REVERT: D 351 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.4751 (mm-30) REVERT: D 353 ARG cc_start: 0.8951 (mtt180) cc_final: 0.8738 (mtt180) REVERT: E 165 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: E 310 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: K 141 TYR cc_start: 0.8411 (t80) cc_final: 0.8048 (t80) REVERT: M 174 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8677 (tpp) REVERT: N 167 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8465 (mmt180) REVERT: O 158 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9036 (ptm) REVERT: O 260 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8888 (mtmm) REVERT: P 311 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: Q 259 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: Q 307 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5881 (mtt) REVERT: Q 353 ARG cc_start: 0.6678 (tmm-80) cc_final: 0.5194 (tmm-80) REVERT: R 133 ASP cc_start: 0.2743 (OUTLIER) cc_final: 0.1082 (m-30) REVERT: R 259 GLU cc_start: 0.8326 (tp30) cc_final: 0.7988 (tp30) REVERT: R 260 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8005 (ttpp) REVERT: R 337 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.3608 (t80) REVERT: S 158 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8410 (ptp) REVERT: S 181 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: S 269 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8775 (mmtt) REVERT: F 296 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8416 (tt0) REVERT: F 319 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7585 (mp) REVERT: H 301 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8878 (pt0) REVERT: H 307 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: J 307 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8335 (tt0) outliers start: 201 outliers final: 98 residues processed: 508 average time/residue: 1.3486 time to fit residues: 829.4187 Evaluate side-chains 491 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 365 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 85 THR 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 219 PHE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 ILE 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 143 ASN Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 167 ARG 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 331 THR Chi-restraints excluded: chain B residue 351 GLU 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 346 ILE Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 282 SER 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 E residue 322 ASP 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 L residue 21 ASP 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 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 92 LYS Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 167 ARG Chi-restraints excluded: chain N residue 236 ILE 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 135 THR Chi-restraints excluded: chain O residue 158 MET 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 158 MET Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 311 GLU 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 260 LYS 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 R residue 113 GLU Chi-restraints excluded: chain R residue 133 ASP 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 73 THR Chi-restraints excluded: chain S residue 158 MET Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 269 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 286 optimal weight: 0.9980 chunk 400 optimal weight: 5.9990 chunk 15 optimal weight: 0.0040 chunk 240 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 321 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 253 GLN M 183 ASN ** N 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085914 restraints weight = 57142.997| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.28 r_work: 0.3058 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1531 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= 0.110 Angle : 0.491 9.708 45775 Z= 0.259 Chirality : 0.044 0.176 5176 Planarity : 0.004 0.047 6008 Dihedral : 4.950 58.682 4658 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.52 % Allowed : 24.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.13), residues: 4287 helix: 1.75 (0.16), residues: 990 sheet: 0.08 (0.15), residues: 1075 loop : -0.85 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 232 HIS 0.001 0.000 HIS L 93 PHE 0.015 0.001 PHE L 169 TYR 0.016 0.001 TYR S 197 ARG 0.006 0.000 ARG Q 206 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 1182) hydrogen bonds : angle 5.14096 ( 3243) covalent geometry : bond 0.00257 (33626) covalent geometry : angle 0.49135 (45775) *********************** 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 549 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 392 time to evaluate : 3.521 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8555 (t0) REVERT: A 353 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7583 (tpm170) REVERT: B 172 ARG cc_start: 0.8336 (mpp-170) cc_final: 0.7952 (mpp-170) REVERT: B 197 TYR cc_start: 0.9143 (m-80) cc_final: 0.8848 (m-80) REVERT: B 288 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8867 (tp30) REVERT: B 351 GLU cc_start: 0.4385 (OUTLIER) cc_final: 0.4154 (tp30) REVERT: C 95 THR cc_start: 0.7857 (m) cc_final: 0.7433 (p) REVERT: C 310 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: C 351 GLU cc_start: 0.5286 (mm-30) cc_final: 0.4840 (mt-10) REVERT: D 196 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9212 (m-80) REVERT: D 267 THR cc_start: 0.9523 (t) cc_final: 0.8969 (m) REVERT: E 310 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: E 351 GLU cc_start: 0.4991 (OUTLIER) cc_final: 0.3242 (tp30) REVERT: K 141 TYR cc_start: 0.8333 (t80) cc_final: 0.8056 (t80) REVERT: L 102 ASP cc_start: 0.8189 (t0) cc_final: 0.7881 (t0) REVERT: M 68 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8791 (mmtp) REVERT: M 174 MET cc_start: 0.9203 (ttp) cc_final: 0.8684 (tpp) REVERT: N 167 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8080 (mmt-90) REVERT: P 241 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: P 289 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: P 311 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: Q 344 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8888 (mptm) REVERT: Q 353 ARG cc_start: 0.6612 (tmm-80) cc_final: 0.5125 (tmm-80) REVERT: R 92 LYS cc_start: 0.8387 (ptpp) cc_final: 0.7974 (ptpp) REVERT: R 174 ASN cc_start: 0.8699 (t0) cc_final: 0.8485 (t0) REVERT: R 181 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: R 196 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: R 259 GLU cc_start: 0.8172 (tp30) cc_final: 0.7884 (tp30) REVERT: R 260 LYS cc_start: 0.8655 (mtpp) cc_final: 0.7996 (ttpp) REVERT: R 337 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.4015 (t80) REVERT: S 174 ASN cc_start: 0.8162 (t0) cc_final: 0.7883 (t0) REVERT: S 181 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: S 269 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8607 (mmtt) REVERT: F 300 SER cc_start: 0.9299 (p) cc_final: 0.9011 (p) REVERT: F 319 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7527 (mp) REVERT: H 301 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8889 (pt0) REVERT: H 307 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: J 307 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8346 (tt0) outliers start: 157 outliers final: 73 residues processed: 508 average time/residue: 1.4001 time to fit residues: 849.7671 Evaluate side-chains 471 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 376 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 365 THR 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 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 C residue 101 ASP Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 219 PHE 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 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 284 SER 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 35 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 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 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 196 SER 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 135 THR 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 148 ARG Chi-restraints excluded: chain P residue 241 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 277 THR 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 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 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 181 GLN Chi-restraints excluded: chain S residue 269 LYS Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain S residue 340 LEU 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 307 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 11 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 chunk 366 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 M 183 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.085506 restraints weight = 57977.763| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.30 r_work: 0.3018 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33626 Z= 0.204 Angle : 0.541 10.307 45775 Z= 0.283 Chirality : 0.045 0.180 5176 Planarity : 0.004 0.046 6008 Dihedral : 4.997 58.086 4656 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.84 % Allowed : 24.15 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4287 helix: 1.56 (0.16), residues: 1006 sheet: 0.08 (0.16), residues: 1058 loop : -0.86 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 232 HIS 0.002 0.001 HIS L 93 PHE 0.012 0.002 PHE K 118 TYR 0.016 0.002 TYR S 197 ARG 0.009 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 1182) hydrogen bonds : angle 5.23345 ( 3243) covalent geometry : bond 0.00489 (33626) covalent geometry : angle 0.54078 (45775) *********************** 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 546 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 378 time to evaluate : 3.823 Fit side-chains REVERT: A 83 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8600 (pp) REVERT: A 255 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7579 (t0) REVERT: B 83 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8440 (pp) REVERT: B 172 ARG cc_start: 0.8369 (mpp-170) cc_final: 0.8005 (mpp-170) REVERT: B 197 TYR cc_start: 0.9176 (m-80) cc_final: 0.8865 (m-80) REVERT: B 288 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8846 (tp30) REVERT: B 351 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.4330 (tp30) REVERT: B 353 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7894 (mtp85) REVERT: B 355 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8955 (ptmt) REVERT: C 95 THR cc_start: 0.8085 (m) cc_final: 0.7658 (p) REVERT: C 109 VAL cc_start: 0.8941 (p) cc_final: 0.8686 (m) REVERT: C 310 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: C 351 GLU cc_start: 0.5218 (OUTLIER) cc_final: 0.4664 (mt-10) REVERT: D 267 THR cc_start: 0.9568 (t) cc_final: 0.8971 (m) REVERT: D 351 GLU cc_start: 0.5424 (mm-30) cc_final: 0.4987 (mm-30) REVERT: E 83 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8532 (pp) REVERT: E 310 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: E 313 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: E 351 GLU cc_start: 0.5020 (OUTLIER) cc_final: 0.3002 (tp30) REVERT: K 141 TYR cc_start: 0.8376 (t80) cc_final: 0.8012 (t80) REVERT: K 211 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: M 68 LYS cc_start: 0.9079 (mmtp) cc_final: 0.8861 (mttp) REVERT: M 174 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8962 (ttp) REVERT: N 158 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9246 (ppp) REVERT: N 167 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.7963 (mmt-90) REVERT: N 179 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9153 (mttp) REVERT: N 311 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7582 (pp20) REVERT: P 289 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: P 311 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: Q 307 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5823 (mtt) REVERT: Q 344 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8875 (mptm) REVERT: R 92 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8133 (ptmm) REVERT: R 181 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: R 196 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: R 260 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8254 (ttpp) REVERT: R 337 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.4025 (t80) REVERT: S 174 ASN cc_start: 0.8166 (t0) cc_final: 0.7857 (t0) REVERT: S 181 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: S 269 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8665 (mmtt) REVERT: F 300 SER cc_start: 0.9287 (p) cc_final: 0.9039 (p) REVERT: F 319 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7504 (mp) REVERT: H 301 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8866 (pt0) REVERT: H 307 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: J 307 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8396 (tt0) outliers start: 168 outliers final: 96 residues processed: 501 average time/residue: 1.4329 time to fit residues: 871.4707 Evaluate side-chains 493 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 366 time to evaluate : 3.848 ------------------------------------------------------------------------------- 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 85 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 255 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 ILE 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 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 353 ARG Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 351 GLU 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 E residue 83 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 143 ASN 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 284 SER Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 346 ILE 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 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 211 GLN Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 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 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 205 THR Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 158 MET 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 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 225 GLN 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 148 ARG 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 P residue 337 PHE Chi-restraints excluded: chain P residue 340 LEU 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 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 78 THR Chi-restraints excluded: chain R residue 93 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 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 269 LYS Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain S residue 340 LEU 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 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 276 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 346 optimal weight: 0.9980 chunk 297 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 417 optimal weight: 0.0040 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN M 183 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088313 restraints weight = 57712.290| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.30 r_work: 0.3065 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1642 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= 0.103 Angle : 0.484 9.057 45775 Z= 0.254 Chirality : 0.043 0.169 5176 Planarity : 0.003 0.044 6008 Dihedral : 4.765 58.848 4656 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.44 % Allowed : 24.73 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 4287 helix: 1.83 (0.16), residues: 1003 sheet: 0.18 (0.16), residues: 1046 loop : -0.79 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 232 HIS 0.002 0.000 HIS M 93 PHE 0.013 0.001 PHE L 169 TYR 0.017 0.001 TYR D 279 ARG 0.010 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 1182) hydrogen bonds : angle 4.98872 ( 3243) covalent geometry : bond 0.00242 (33626) covalent geometry : angle 0.48387 (45775) *********************** 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 537 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 383 time to evaluate : 3.605 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8432 (p0) REVERT: A 353 ARG cc_start: 0.8684 (mtt90) cc_final: 0.7445 (tpm170) REVERT: B 83 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8202 (pp) REVERT: B 172 ARG cc_start: 0.8356 (mpp-170) cc_final: 0.7987 (mpp-170) REVERT: B 197 TYR cc_start: 0.9072 (m-80) cc_final: 0.8777 (m-80) REVERT: B 351 GLU cc_start: 0.4388 (OUTLIER) cc_final: 0.4165 (tp30) REVERT: B 355 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8927 (ptmt) REVERT: B 365 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8930 (t) REVERT: C 95 THR cc_start: 0.7878 (m) cc_final: 0.7473 (p) REVERT: C 109 VAL cc_start: 0.8846 (p) cc_final: 0.8582 (m) REVERT: C 310 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: C 351 GLU cc_start: 0.5279 (OUTLIER) cc_final: 0.4887 (mm-30) REVERT: D 267 THR cc_start: 0.9530 (t) cc_final: 0.9036 (m) REVERT: D 351 GLU cc_start: 0.5081 (mm-30) cc_final: 0.4784 (mm-30) REVERT: D 365 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.8939 (t) REVERT: E 310 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: E 351 GLU cc_start: 0.5003 (OUTLIER) cc_final: 0.3392 (tp30) REVERT: K 141 TYR cc_start: 0.8300 (t80) cc_final: 0.8077 (t80) REVERT: M 174 MET cc_start: 0.9189 (ttp) cc_final: 0.8636 (tpp) REVERT: N 311 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7572 (pp20) REVERT: O 101 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: O 196 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.7373 (t80) REVERT: O 260 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8888 (mtmm) REVERT: P 289 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: P 311 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: P 382 ILE cc_start: 0.7983 (pp) cc_final: 0.7743 (pp) REVERT: Q 344 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8880 (mptm) REVERT: Q 353 ARG cc_start: 0.6162 (tmm-80) cc_final: 0.4834 (tmm-80) REVERT: R 92 LYS cc_start: 0.8388 (ptpp) cc_final: 0.7894 (ptpp) REVERT: R 121 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7945 (mp) REVERT: R 174 ASN cc_start: 0.8657 (t0) cc_final: 0.8452 (t0) REVERT: R 181 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8063 (mm110) REVERT: R 260 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8009 (ttpp) REVERT: R 295 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8585 (ttp80) REVERT: R 337 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.4052 (t80) REVERT: S 174 ASN cc_start: 0.8161 (t0) cc_final: 0.7794 (t0) REVERT: S 181 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: S 269 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8789 (mmtp) REVERT: F 300 SER cc_start: 0.9287 (p) cc_final: 0.9032 (p) REVERT: F 319 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7468 (mp) REVERT: H 307 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: J 307 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8323 (tt0) outliers start: 154 outliers final: 88 residues processed: 497 average time/residue: 1.3882 time to fit residues: 831.2464 Evaluate side-chains 487 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 375 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU 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 355 LYS 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 302 LEU Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 351 GLU 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 322 ASP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 365 THR 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 284 SER 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 108 TYR 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 44 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 117 GLU 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 365 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 133 ASP Chi-restraints excluded: chain O residue 135 THR Chi-restraints excluded: chain O residue 196 PHE Chi-restraints excluded: chain O residue 260 LYS 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 148 ARG 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 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 78 THR Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 121 ILE 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 S residue 181 GLN Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 269 LYS 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 G residue 322 LEU 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 307 GLU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 287 VAL 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 172 optimal weight: 0.4980 chunk 118 optimal weight: 6.9990 chunk 370 optimal weight: 8.9990 chunk 189 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 364 optimal weight: 0.8980 chunk 347 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN M 183 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 R 115 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 = 0.3491 r_free = 0.3491 target = 0.106993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.088995 restraints weight = 57653.992| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.29 r_work: 0.3077 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1707 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= 0.105 Angle : 0.481 10.074 45775 Z= 0.252 Chirality : 0.043 0.167 5176 Planarity : 0.003 0.044 6008 Dihedral : 4.651 59.361 4654 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.18 % Allowed : 24.90 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4287 helix: 1.97 (0.17), residues: 995 sheet: 0.23 (0.16), residues: 1026 loop : -0.78 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 232 HIS 0.002 0.000 HIS M 93 PHE 0.011 0.001 PHE P 319 TYR 0.018 0.001 TYR D 279 ARG 0.011 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 1182) hydrogen bonds : angle 4.90279 ( 3243) covalent geometry : bond 0.00247 (33626) covalent geometry : angle 0.48104 (45775) *********************** 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 531 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 386 time to evaluate : 3.446 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8526 (pp) REVERT: A 136 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8409 (p0) REVERT: A 353 ARG cc_start: 0.8673 (mtt90) cc_final: 0.7451 (tpm170) REVERT: B 83 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8142 (pp) REVERT: B 172 ARG cc_start: 0.8340 (mpp-170) cc_final: 0.7957 (mpp-170) REVERT: B 197 TYR cc_start: 0.9083 (m-80) cc_final: 0.8791 (m-80) REVERT: B 355 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8930 (ptmt) REVERT: B 365 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9016 (t) REVERT: C 95 THR cc_start: 0.7758 (m) cc_final: 0.7377 (p) REVERT: C 109 VAL cc_start: 0.8864 (p) cc_final: 0.8590 (m) REVERT: C 310 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: C 351 GLU cc_start: 0.5403 (OUTLIER) cc_final: 0.4854 (mt-10) REVERT: D 196 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.9236 (m-80) REVERT: D 267 THR cc_start: 0.9502 (t) cc_final: 0.9263 (m) REVERT: D 351 GLU cc_start: 0.5102 (mm-30) cc_final: 0.4765 (mm-30) REVERT: D 365 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.8939 (t) REVERT: E 310 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: E 351 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.3464 (tp30) REVERT: K 141 TYR cc_start: 0.8342 (t80) cc_final: 0.8052 (t80) REVERT: L 102 ASP cc_start: 0.8179 (t0) cc_final: 0.7878 (t0) REVERT: M 1 MET cc_start: 0.7008 (mmt) cc_final: 0.6238 (mmt) REVERT: M 174 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8636 (tpp) REVERT: N 311 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7549 (pp20) REVERT: O 196 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.7392 (t80) REVERT: P 289 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: P 311 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: Q 307 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.5776 (mtt) REVERT: R 92 LYS cc_start: 0.8403 (ptpp) cc_final: 0.7900 (ptpp) REVERT: R 121 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8048 (mm) REVERT: R 133 ASP cc_start: 0.3174 (OUTLIER) cc_final: 0.1701 (m-30) REVERT: R 181 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8056 (mm110) REVERT: R 260 LYS cc_start: 0.8579 (mtpp) cc_final: 0.7855 (ttpp) REVERT: R 295 ARG cc_start: 0.8968 (ttp80) cc_final: 0.8632 (ttp80) REVERT: R 337 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.4154 (t80) REVERT: S 174 ASN cc_start: 0.8189 (t0) cc_final: 0.7887 (t0) REVERT: S 181 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: S 269 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8916 (mmtp) REVERT: F 319 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7493 (mp) REVERT: I 295 GLN cc_start: 0.7604 (mm110) cc_final: 0.6606 (mt0) REVERT: J 301 GLU cc_start: 0.8509 (pt0) cc_final: 0.8263 (pt0) REVERT: J 307 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8339 (tt0) outliers start: 145 outliers final: 79 residues processed: 490 average time/residue: 1.3446 time to fit residues: 791.9916 Evaluate side-chains 478 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 374 time to evaluate : 3.370 ------------------------------------------------------------------------------- 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 85 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 136 ASN Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 165 GLU 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 355 LYS 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 302 LEU Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 196 PHE 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 322 ASP Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 365 THR 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 284 SER Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 346 ILE 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 108 TYR 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 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 311 GLU Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 196 PHE 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 106 ILE Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 148 ARG 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 239 ILE 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 R residue 78 THR Chi-restraints excluded: chain R residue 121 ILE 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 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 S residue 181 GLN Chi-restraints excluded: chain S residue 269 LYS Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 287 VAL 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 303 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 391 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN M 183 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 ** 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 = 0.3459 r_free = 0.3459 target = 0.104339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.086376 restraints weight = 57122.740| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.29 r_work: 0.3062 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1732 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= 0.125 Angle : 0.497 13.189 45775 Z= 0.258 Chirality : 0.043 0.170 5176 Planarity : 0.003 0.043 6008 Dihedral : 4.647 59.515 4652 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.92 % Allowed : 25.22 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4287 helix: 1.91 (0.16), residues: 1003 sheet: 0.20 (0.16), residues: 1057 loop : -0.77 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 232 HIS 0.001 0.000 HIS B 134 PHE 0.011 0.001 PHE L 169 TYR 0.017 0.001 TYR D 279 ARG 0.010 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 1182) hydrogen bonds : angle 4.92113 ( 3243) covalent geometry : bond 0.00299 (33626) covalent geometry : angle 0.49744 (45775) *********************** 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 518 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 382 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8539 (pp) REVERT: A 136 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8533 (p0) REVERT: A 353 ARG cc_start: 0.8680 (mtt90) cc_final: 0.7451 (tpm170) REVERT: B 83 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8232 (pp) REVERT: B 172 ARG cc_start: 0.8372 (mpp-170) cc_final: 0.7977 (mpp-170) REVERT: B 197 TYR cc_start: 0.9082 (m-80) cc_final: 0.8789 (m-80) REVERT: B 355 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8906 (ptmt) REVERT: B 365 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9005 (t) REVERT: C 95 THR cc_start: 0.7660 (m) cc_final: 0.7296 (p) REVERT: C 109 VAL cc_start: 0.8844 (p) cc_final: 0.8561 (m) REVERT: C 310 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: C 351 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4510 (mt-10) REVERT: D 267 THR cc_start: 0.9507 (t) cc_final: 0.9266 (m) REVERT: D 351 GLU cc_start: 0.5185 (mm-30) cc_final: 0.4812 (mm-30) REVERT: D 365 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8939 (t) REVERT: E 94 MET cc_start: 0.8288 (tpp) cc_final: 0.8065 (mmt) REVERT: E 95 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8562 (t) REVERT: E 260 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8516 (mtmt) REVERT: E 310 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: E 351 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.3394 (tp30) REVERT: K 141 TYR cc_start: 0.8293 (t80) cc_final: 0.8022 (t80) REVERT: K 174 MET cc_start: 0.8916 (ttp) cc_final: 0.8393 (tpp) REVERT: M 1 MET cc_start: 0.6966 (mmt) cc_final: 0.6229 (mmt) REVERT: M 174 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8909 (ttp) REVERT: N 311 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7534 (pp20) REVERT: O 196 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.7404 (t80) REVERT: P 289 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: P 311 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: P 382 ILE cc_start: 0.8071 (pp) cc_final: 0.7843 (pp) REVERT: R 92 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8103 (ptmm) REVERT: R 121 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8050 (mm) REVERT: R 133 ASP cc_start: 0.3419 (OUTLIER) cc_final: 0.1764 (m-30) REVERT: R 181 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8064 (mm110) REVERT: R 259 GLU cc_start: 0.8064 (tp30) cc_final: 0.7791 (tp30) REVERT: R 260 LYS cc_start: 0.8505 (mtpp) cc_final: 0.7681 (ttpp) REVERT: R 337 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.4060 (t80) REVERT: S 174 ASN cc_start: 0.8194 (t0) cc_final: 0.7899 (t0) REVERT: S 181 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: S 269 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8932 (mmtp) REVERT: F 319 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7450 (mp) REVERT: I 295 GLN cc_start: 0.7640 (mm110) cc_final: 0.6580 (mt0) REVERT: J 301 GLU cc_start: 0.8531 (pt0) cc_final: 0.8271 (pt0) REVERT: J 307 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8367 (tt0) outliers start: 136 outliers final: 81 residues processed: 485 average time/residue: 1.3271 time to fit residues: 777.0984 Evaluate side-chains 475 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 370 time to evaluate : 3.463 ------------------------------------------------------------------------------- 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 85 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 136 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 346 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 165 GLU 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 355 LYS 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 302 LEU Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 351 GLU 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 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 284 SER Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 346 ILE 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 108 TYR Chi-restraints excluded: chain K residue 129 ILE 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 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 311 GLU Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 196 PHE 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 106 ILE Chi-restraints excluded: chain P residue 148 ARG 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 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 121 ILE 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 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 S residue 181 GLN Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 269 LYS Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain J residue 287 VAL 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 210 optimal weight: 10.0000 chunk 313 optimal weight: 0.6980 chunk 296 optimal weight: 10.0000 chunk 409 optimal weight: 10.0000 chunk 287 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 404 optimal weight: 30.0000 chunk 320 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN M 183 ASN ** N 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN 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 = 0.3465 r_free = 0.3465 target = 0.104568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086692 restraints weight = 56908.016| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.26 r_work: 0.3045 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33626 Z= 0.159 Angle : 0.519 11.462 45775 Z= 0.270 Chirality : 0.044 0.169 5176 Planarity : 0.004 0.043 6008 Dihedral : 4.740 59.248 4652 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.43 % Allowed : 25.71 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.13), residues: 4287 helix: 1.84 (0.16), residues: 1003 sheet: 0.14 (0.16), residues: 1082 loop : -0.74 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 112 HIS 0.001 0.000 HIS R 134 PHE 0.011 0.001 PHE P 319 TYR 0.018 0.002 TYR S 197 ARG 0.010 0.000 ARG Q 206 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 1182) hydrogen bonds : angle 5.00660 ( 3243) covalent geometry : bond 0.00381 (33626) covalent geometry : angle 0.51932 (45775) ********************** 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 493 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 374 time to evaluate : 3.655 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8557 (pp) REVERT: A 255 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7504 (t0) REVERT: A 267 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8999 (m) REVERT: B 83 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8369 (pp) REVERT: B 172 ARG cc_start: 0.8374 (mpp-170) cc_final: 0.7977 (mpp-170) REVERT: B 197 TYR cc_start: 0.9086 (m-80) cc_final: 0.8792 (m-80) REVERT: B 355 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8913 (ptmt) REVERT: B 365 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.9025 (t) REVERT: C 95 THR cc_start: 0.7797 (m) cc_final: 0.7445 (p) REVERT: C 109 VAL cc_start: 0.8891 (p) cc_final: 0.8640 (m) REVERT: C 310 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: C 351 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4687 (mm-30) REVERT: D 113 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7366 (pp20) REVERT: D 267 THR cc_start: 0.9406 (t) cc_final: 0.9187 (m) REVERT: D 351 GLU cc_start: 0.5326 (OUTLIER) cc_final: 0.4912 (mm-30) REVERT: D 365 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8952 (t) REVERT: E 260 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8542 (mtmt) REVERT: E 310 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: K 141 TYR cc_start: 0.8338 (t80) cc_final: 0.8101 (t80) REVERT: K 174 MET cc_start: 0.8906 (ttp) cc_final: 0.8367 (tpp) REVERT: L 120 ASP cc_start: 0.7916 (m-30) cc_final: 0.7590 (m-30) REVERT: M 1 MET cc_start: 0.6945 (mmt) cc_final: 0.6252 (mmt) REVERT: M 174 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8928 (ttp) REVERT: N 311 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: O 260 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8904 (mtmm) REVERT: P 289 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: P 311 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: P 324 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8460 (t0) REVERT: R 92 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8106 (ptmm) REVERT: R 113 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: R 121 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8145 (mm) REVERT: R 133 ASP cc_start: 0.3863 (OUTLIER) cc_final: 0.2343 (m-30) REVERT: R 181 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8071 (mm110) REVERT: R 259 GLU cc_start: 0.8150 (tp30) cc_final: 0.7825 (tp30) REVERT: R 260 LYS cc_start: 0.8552 (mtpp) cc_final: 0.7763 (ttpp) REVERT: R 295 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8617 (ttp80) REVERT: R 337 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.4184 (t80) REVERT: S 174 ASN cc_start: 0.8183 (t0) cc_final: 0.7959 (t0) REVERT: S 181 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: F 319 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7544 (mp) REVERT: J 301 GLU cc_start: 0.8668 (pt0) cc_final: 0.8389 (pt0) REVERT: J 307 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8253 (tt0) outliers start: 119 outliers final: 81 residues processed: 468 average time/residue: 1.3254 time to fit residues: 747.5844 Evaluate side-chains 472 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 365 time to evaluate : 3.454 ------------------------------------------------------------------------------- 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 85 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 255 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 165 GLU 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 355 LYS 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 302 LEU Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 113 GLU 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 D residue 365 THR 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 284 SER Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 346 ILE 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 108 TYR Chi-restraints excluded: chain K residue 129 ILE 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 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 311 GLU Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 260 LYS 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 106 ILE Chi-restraints excluded: chain P residue 148 ARG Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 294 MET Chi-restraints excluded: chain P residue 311 GLU Chi-restraints excluded: chain P residue 324 ASN Chi-restraints excluded: chain P residue 340 LEU 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 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 121 ILE Chi-restraints excluded: chain R residue 133 ASP 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 347 THR Chi-restraints excluded: chain S residue 181 GLN Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 327 VAL Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 287 VAL 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 344 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 416 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 388 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 183 ASN ** N 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN Q 212 ASN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.085241 restraints weight = 57149.083| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.28 r_work: 0.3045 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33626 Z= 0.158 Angle : 0.522 12.916 45775 Z= 0.271 Chirality : 0.044 0.176 5176 Planarity : 0.004 0.048 6008 Dihedral : 4.761 59.172 4652 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.63 % Allowed : 25.59 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 4287 helix: 1.82 (0.16), residues: 1003 sheet: 0.12 (0.16), residues: 1082 loop : -0.75 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 142 HIS 0.001 0.000 HIS R 134 PHE 0.011 0.001 PHE P 319 TYR 0.018 0.002 TYR D 279 ARG 0.012 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 1182) hydrogen bonds : angle 5.01441 ( 3243) covalent geometry : bond 0.00379 (33626) covalent geometry : angle 0.52158 (45775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25913.07 seconds wall clock time: 446 minutes 9.14 seconds (26769.14 seconds total)