Starting phenix.real_space_refine on Sat Feb 7 09:45:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvd_52432/02_2026/9hvd_52432.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvd_52432/02_2026/9hvd_52432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hvd_52432/02_2026/9hvd_52432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvd_52432/02_2026/9hvd_52432.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvd_52432/02_2026/9hvd_52432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvd_52432/02_2026/9hvd_52432.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 175 5.16 5 C 19834 2.51 5 N 5447 2.21 5 O 5848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31306 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3077 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain breaks: 3 Chain: "K" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1507 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "J" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3428 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 21, 'TRANS': 416} Chain breaks: 1 Chain: "D" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2540 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Chain: "B" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2270 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 282} Chain breaks: 1 Chain: "G" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2676 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 17, 'TRANS': 326} Chain: "E" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3352 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 1 Chain: "I" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3440 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 1 Chain: "C" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2279 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Chain: "H" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2676 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 326} Chain: "L" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1507 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Time building chain proxies: 7.27, per 1000 atoms: 0.23 Number of scatterers: 31306 At special positions: 0 Unit cell: (196.9, 181.5, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 175 16.00 P 2 15.00 O 5848 8.00 N 5447 7.00 C 19834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS K 70 " - pdb=" SG CYS K 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS L 70 " - pdb=" SG CYS L 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7562 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 42 sheets defined 42.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'F' and resid 36 through 47 removed outlier: 3.689A pdb=" N GLY F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 64 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 94 through 97 Processing helix chain 'F' and resid 114 through 124 Processing helix chain 'F' and resid 208 through 217 removed outlier: 4.403A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP F 213 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 236 removed outlier: 4.920A pdb=" N ILE F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Proline residue: F 230 - end of helix Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 316 through 334 removed outlier: 4.426A pdb=" N MET F 320 " --> pdb=" O LEU F 316 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU F 321 " --> pdb=" O GLY F 317 " (cutoff:3.500A) Proline residue: F 327 - end of helix removed outlier: 4.077A pdb=" N ALA F 332 " --> pdb=" O LYS F 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 52 through 58 removed outlier: 3.766A pdb=" N ARG K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 120 removed outlier: 3.517A pdb=" N LYS K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL K 118 " --> pdb=" O HIS K 114 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU K 119 " --> pdb=" O VAL K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 142 removed outlier: 4.843A pdb=" N TRP K 136 " --> pdb=" O GLN K 132 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL K 137 " --> pdb=" O ARG K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 157 Processing helix chain 'K' and resid 160 through 166 removed outlier: 3.814A pdb=" N ASP K 164 " --> pdb=" O PRO K 160 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU K 166 " --> pdb=" O ILE K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 184 removed outlier: 3.740A pdb=" N VAL K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 67 Processing helix chain 'J' and resid 76 through 86 removed outlier: 3.617A pdb=" N THR J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.838A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 113 removed outlier: 3.629A pdb=" N CYS J 112 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 161 through 175 Processing helix chain 'J' and resid 228 through 234 removed outlier: 3.879A pdb=" N GLN J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 263 removed outlier: 3.839A pdb=" N GLN J 258 " --> pdb=" O PRO J 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN J 263 " --> pdb=" O LEU J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 484 through 489 Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.636A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 97 Processing helix chain 'D' and resid 128 through 146 removed outlier: 3.644A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.756A pdb=" N HIS D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.617A pdb=" N ALA D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.887A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.660A pdb=" N VAL D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.659A pdb=" N LEU D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 removed outlier: 4.044A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU D 274 " --> pdb=" O MET D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 274' Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.794A pdb=" N GLU D 293 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.656A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 321' Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 345 through 350 removed outlier: 3.559A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL D 350 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.981A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 removed outlier: 3.509A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.682A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 77 removed outlier: 4.256A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 105 removed outlier: 3.625A pdb=" N CYS B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 159 through 170 removed outlier: 4.204A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.982A pdb=" N MET B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 222 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.508A pdb=" N PHE B 235 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.504A pdb=" N TYR B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.585A pdb=" N LEU B 280 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 281 " --> pdb=" O PRO B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 281' Processing helix chain 'B' and resid 292 through 304 removed outlier: 3.913A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 217 Processing helix chain 'G' and resid 223 through 239 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.026A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS G 257 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 287 removed outlier: 3.547A pdb=" N VAL G 287 " --> pdb=" O GLU G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 312 removed outlier: 3.650A pdb=" N ILE G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 324 Processing helix chain 'G' and resid 325 through 327 No H-bonds generated for 'chain 'G' and resid 325 through 327' Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'G' and resid 368 through 380 removed outlier: 4.485A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.950A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU G 395 " --> pdb=" O ALA G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 390 through 395' Processing helix chain 'G' and resid 419 through 430 Processing helix chain 'G' and resid 439 through 443 removed outlier: 3.824A pdb=" N PHE G 443 " --> pdb=" O THR G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 464 removed outlier: 3.719A pdb=" N ASP G 462 " --> pdb=" O ASP G 459 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU G 463 " --> pdb=" O PRO G 460 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN G 464 " --> pdb=" O ASP G 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 459 through 464' Processing helix chain 'G' and resid 475 through 479 Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 517 removed outlier: 3.832A pdb=" N VAL G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.712A pdb=" N ASP E 18 " --> pdb=" O ARG E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.652A pdb=" N LEU E 27 " --> pdb=" O PRO E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 removed outlier: 3.780A pdb=" N LEU E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.820A pdb=" N ILE E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.680A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 236 Processing helix chain 'E' and resid 262 through 267 removed outlier: 3.676A pdb=" N ILE E 267 " --> pdb=" O TYR E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 322 removed outlier: 3.929A pdb=" N MET E 320 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 334 removed outlier: 3.730A pdb=" N LEU E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 67 Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.575A pdb=" N THR I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU I 80 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY I 87 " --> pdb=" O LEU I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.704A pdb=" N ILE I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 229 through 231 No H-bonds generated for 'chain 'I' and resid 229 through 231' Processing helix chain 'I' and resid 253 through 263 removed outlier: 4.340A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN I 258 " --> pdb=" O PRO I 254 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN I 263 " --> pdb=" O LEU I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 279 removed outlier: 3.560A pdb=" N PHE I 272 " --> pdb=" O THR I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 484 through 489 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.921A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.747A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.533A pdb=" N GLU C 157 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 removed outlier: 3.519A pdb=" N ALA C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 removed outlier: 3.696A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.552A pdb=" N VAL C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.560A pdb=" N LEU C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.891A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.598A pdb=" N GLU C 293 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.625A pdb=" N GLU C 299 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.686A pdb=" N LEU C 320 " --> pdb=" O PRO C 317 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 317 through 321' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.528A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.833A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.563A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.895A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 4.293A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 105 removed outlier: 3.683A pdb=" N CYS A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.675A pdb=" N LYS A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 159 through 170 removed outlier: 4.248A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 170 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.750A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 222 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.959A pdb=" N VAL A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.528A pdb=" N LYS A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.656A pdb=" N ILE A 281 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.506A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 196 removed outlier: 3.774A pdb=" N PHE H 195 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET H 196 " --> pdb=" O THR H 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 192 through 196' Processing helix chain 'H' and resid 204 through 215 removed outlier: 3.864A pdb=" N SER H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 239 removed outlier: 3.594A pdb=" N ASP H 239 " --> pdb=" O GLN H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 267 removed outlier: 3.790A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS H 257 " --> pdb=" O VAL H 253 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 287 removed outlier: 3.595A pdb=" N VAL H 287 " --> pdb=" O GLU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 312 removed outlier: 3.549A pdb=" N ILE H 312 " --> pdb=" O VAL H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 324 Processing helix chain 'H' and resid 325 through 327 No H-bonds generated for 'chain 'H' and resid 325 through 327' Processing helix chain 'H' and resid 339 through 352 Processing helix chain 'H' and resid 368 through 380 removed outlier: 4.265A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.937A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 390 through 395' Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 459 through 464 removed outlier: 3.515A pdb=" N ASP H 462 " --> pdb=" O ASP H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 497 removed outlier: 3.585A pdb=" N VAL H 497 " --> pdb=" O PRO H 494 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 510 No H-bonds generated for 'chain 'H' and resid 508 through 510' Processing helix chain 'H' and resid 511 through 518 removed outlier: 4.545A pdb=" N VAL H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 52 through 57 removed outlier: 3.880A pdb=" N ARG L 57 " --> pdb=" O ARG L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 120 removed outlier: 3.712A pdb=" N VAL L 118 " --> pdb=" O HIS L 114 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU L 119 " --> pdb=" O VAL L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 135 removed outlier: 4.013A pdb=" N LEU L 127 " --> pdb=" O LYS L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 142 Processing helix chain 'L' and resid 146 through 157 Processing helix chain 'L' and resid 158 through 165 removed outlier: 6.300A pdb=" N SER L 161 " --> pdb=" O SER L 158 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE L 162 " --> pdb=" O ASP L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 184 removed outlier: 3.833A pdb=" N VAL L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.512A pdb=" N VAL F 54 " --> pdb=" O VAL F 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AA3, first strand: chain 'F' and resid 108 through 110 Processing sheet with id=AA4, first strand: chain 'F' and resid 199 through 202 removed outlier: 4.208A pdb=" N LEU F 131 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU F 128 " --> pdb=" O TYR F 301 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N HIS F 303 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N MET F 130 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N MET F 305 " --> pdb=" O MET F 130 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET F 132 " --> pdb=" O MET F 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 167 through 172 removed outlier: 3.567A pdb=" N ILE F 193 " --> pdb=" O VAL J 240 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL J 240 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL J 202 " --> pdb=" O PHE J 215 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE J 215 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 179 through 183 Processing sheet with id=AA7, first strand: chain 'F' and resid 370 through 371 removed outlier: 6.295A pdb=" N THR F 386 " --> pdb=" O ILE F 404 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN F 403 " --> pdb=" O ILE F 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AA9, first strand: chain 'K' and resid 19 through 27 removed outlier: 5.722A pdb=" N VAL K 24 " --> pdb=" O SER K 35 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER K 35 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLU K 43 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU K 85 " --> pdb=" O GLU K 43 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET K 45 " --> pdb=" O LEU K 85 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG K 75 " --> pdb=" O ASP K 84 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER K 86 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL K 73 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 119 through 124 removed outlier: 6.826A pdb=" N THR J 91 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE J 123 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL J 93 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN J 44 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL J 151 " --> pdb=" O GLN J 44 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL J 46 " --> pdb=" O VAL J 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU J 150 " --> pdb=" O SER J 250 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER J 250 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS J 247 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE J 184 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE J 249 " --> pdb=" O THR J 182 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR J 182 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE J 251 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL J 180 " --> pdb=" O ILE J 251 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER J 179 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N HIS J 288 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET J 181 " --> pdb=" O HIS J 288 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS J 290 " --> pdb=" O MET J 181 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET J 183 " --> pdb=" O HIS J 290 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR J 292 " --> pdb=" O MET J 183 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE J 185 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 69 through 70 Processing sheet with id=AB3, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AB4, first strand: chain 'J' and resid 336 through 338 removed outlier: 3.623A pdb=" N ARG J 344 " --> pdb=" O THR J 336 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE J 342 " --> pdb=" O SER J 338 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL J 378 " --> pdb=" O LEU J 396 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL J 430 " --> pdb=" O ILE J 449 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.690A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE J 373 " --> pdb=" O LEU J 391 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL J 390 " --> pdb=" O ILE J 408 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN J 407 " --> pdb=" O LEU J 425 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR J 424 " --> pdb=" O ILE J 441 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU J 443 " --> pdb=" O THR J 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'J' and resid 384 through 385 removed outlier: 6.532A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ARG J 401 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU J 418 " --> pdb=" O VAL J 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 330 through 331 removed outlier: 6.958A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.508A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 246 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.555A pdb=" N SER D 307 " --> pdb=" O TYR H 385 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N LEU H 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL H 332 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU H 402 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU H 334 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU H 403 " --> pdb=" O CYS H 437 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL H 434 " --> pdb=" O LEU H 499 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE H 501 " --> pdb=" O VAL H 434 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 175 through 178 removed outlier: 8.979A pdb=" N THR B 176 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 178 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 152 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 192 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE B 226 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N PHE B 285 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 228 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AC3, first strand: chain 'G' and resid 505 through 507 removed outlier: 7.006A pdb=" N VAL G 434 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE G 501 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 401 " --> pdb=" O LEU G 435 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N CYS G 437 " --> pdb=" O VAL G 401 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU G 403 " --> pdb=" O CYS G 437 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL G 332 " --> pdb=" O LYS G 400 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU G 402 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU G 334 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 307 " --> pdb=" O ALA G 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 407 through 408 removed outlier: 3.565A pdb=" N ALA G 407 " --> pdb=" O MET G 415 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 482 through 484 removed outlier: 6.917A pdb=" N ARG G 483 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 233 " --> pdb=" O MET C 166 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 76 through 77 removed outlier: 6.724A pdb=" N VAL E 53 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 52 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL E 54 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU E 102 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 101 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 207 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 76 through 77 removed outlier: 6.724A pdb=" N VAL E 53 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 52 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL E 54 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU E 102 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 101 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 207 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU E 128 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N HIS E 303 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET E 130 " --> pdb=" O HIS E 303 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N MET E 305 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET E 132 " --> pdb=" O MET E 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 167 through 172 removed outlier: 7.375A pdb=" N LEU E 167 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP E 161 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 193 " --> pdb=" O VAL I 240 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL I 238 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS I 214 " --> pdb=" O ALA I 204 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASP I 206 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL I 212 " --> pdb=" O ASP I 206 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 179 through 182 removed outlier: 3.598A pdb=" N PHE I 226 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE I 224 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 344 through 345 Processing sheet with id=AD2, first strand: chain 'E' and resid 368 through 371 removed outlier: 6.505A pdb=" N SER E 369 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN E 403 " --> pdb=" O ILE E 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 374 through 375 removed outlier: 5.973A pdb=" N VAL E 374 " --> pdb=" O LEU E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 397 through 398 removed outlier: 7.309A pdb=" N THR E 397 " --> pdb=" O ILE E 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 119 through 124 removed outlier: 6.803A pdb=" N THR I 91 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE I 123 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL I 93 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL I 46 " --> pdb=" O VAL I 151 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU I 150 " --> pdb=" O SER I 250 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER I 250 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR I 152 " --> pdb=" O HIS I 248 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N HIS I 248 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS I 247 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE I 184 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE I 249 " --> pdb=" O THR I 182 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR I 182 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE I 251 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL I 180 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER I 179 " --> pdb=" O GLN I 286 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS I 288 " --> pdb=" O SER I 179 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR I 292 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE I 185 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 69 through 70 Processing sheet with id=AD7, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AD8, first strand: chain 'I' and resid 336 through 338 removed outlier: 3.819A pdb=" N ILE I 342 " --> pdb=" O SER I 338 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU I 361 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL I 378 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR I 395 " --> pdb=" O LEU I 413 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.901A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE I 373 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLN I 407 " --> pdb=" O LEU I 425 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR I 424 " --> pdb=" O ILE I 441 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 367 through 368 removed outlier: 6.586A pdb=" N VAL I 367 " --> pdb=" O ILE I 385 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS I 384 " --> pdb=" O VAL I 402 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU I 418 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.585A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 175 through 178 removed outlier: 8.895A pdb=" N THR A 176 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 178 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 152 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA A 123 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR A 151 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 125 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR A 153 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 192 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 206 through 209 Processing sheet with id=AE5, first strand: chain 'H' and resid 407 through 408 removed outlier: 3.635A pdb=" N ALA H 407 " --> pdb=" O MET H 415 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET H 415 " --> pdb=" O ALA H 407 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 27 removed outlier: 5.683A pdb=" N VAL L 24 " --> pdb=" O SER L 35 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER L 35 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU L 43 " --> pdb=" O ILE L 83 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LEU L 85 " --> pdb=" O GLU L 43 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET L 45 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG L 75 " --> pdb=" O ASP L 84 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER L 86 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL L 73 " --> pdb=" O SER L 86 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10382 1.34 - 1.46: 5839 1.46 - 1.58: 15367 1.58 - 1.70: 8 1.70 - 1.82: 264 Bond restraints: 31860 Sorted by residual: bond pdb=" CA PHE C 197 " pdb=" CB PHE C 197 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.55e+00 bond pdb=" CA ASN H 190 " pdb=" CB ASN H 190 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.76e-02 3.23e+03 2.20e+00 bond pdb=" CB LYS F 68 " pdb=" CG LYS F 68 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB LYS H 466 " pdb=" CG LYS H 466 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C TYR F 38 " pdb=" N PRO F 39 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.65e+00 ... (remaining 31855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 42744 2.54 - 5.08: 322 5.08 - 7.61: 45 7.61 - 10.15: 14 10.15 - 12.69: 7 Bond angle restraints: 43132 Sorted by residual: angle pdb=" CA LYS F 68 " pdb=" CB LYS F 68 " pdb=" CG LYS F 68 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CB MET F 84 " pdb=" CG MET F 84 " pdb=" SD MET F 84 " ideal model delta sigma weight residual 112.70 125.39 -12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" CB LYS I 176 " pdb=" CG LYS I 176 " pdb=" CD LYS I 176 " ideal model delta sigma weight residual 111.30 120.96 -9.66 2.30e+00 1.89e-01 1.76e+01 angle pdb=" CB MET L 21 " pdb=" CG MET L 21 " pdb=" SD MET L 21 " ideal model delta sigma weight residual 112.70 125.12 -12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C GLU E 441 " pdb=" N VAL E 442 " pdb=" CA VAL E 442 " ideal model delta sigma weight residual 121.97 129.32 -7.35 1.80e+00 3.09e-01 1.67e+01 ... (remaining 43127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 17294 17.54 - 35.07: 1610 35.07 - 52.61: 433 52.61 - 70.15: 138 70.15 - 87.68: 21 Dihedral angle restraints: 19496 sinusoidal: 7842 harmonic: 11654 Sorted by residual: dihedral pdb=" CA TYR I 319 " pdb=" C TYR I 319 " pdb=" N PRO I 320 " pdb=" CA PRO I 320 " ideal model delta harmonic sigma weight residual 180.00 122.08 57.92 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA PHE I 57 " pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CA PRO I 58 " ideal model delta harmonic sigma weight residual 180.00 144.56 35.44 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA ALA C 195 " pdb=" C ALA C 195 " pdb=" N PRO C 196 " pdb=" CA PRO C 196 " ideal model delta harmonic sigma weight residual 180.00 145.15 34.85 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 19493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3677 0.043 - 0.086: 926 0.086 - 0.129: 407 0.129 - 0.173: 11 0.173 - 0.216: 2 Chirality restraints: 5023 Sorted by residual: chirality pdb=" CA ARG K 53 " pdb=" N ARG K 53 " pdb=" C ARG K 53 " pdb=" CB ARG K 53 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA TYR E 38 " pdb=" N TYR E 38 " pdb=" C TYR E 38 " pdb=" CB TYR E 38 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CB ILE J 161 " pdb=" CA ILE J 161 " pdb=" CG1 ILE J 161 " pdb=" CG2 ILE J 161 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 5020 not shown) Planarity restraints: 5520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR I 319 " 0.087 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO I 320 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO I 320 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO I 320 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 57 " -0.052 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO I 58 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO I 58 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 58 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 57 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO J 58 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO J 58 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 58 " 0.040 5.00e-02 4.00e+02 ... (remaining 5517 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 14863 2.97 - 3.45: 30610 3.45 - 3.93: 47037 3.93 - 4.42: 51683 4.42 - 4.90: 87505 Nonbonded interactions: 231698 Sorted by model distance: nonbonded pdb=" N GLN B 43 " pdb=" OE1 GLN B 43 " model vdw 2.484 3.120 nonbonded pdb=" O TYR F 124 " pdb=" OD1 ASP F 125 " model vdw 2.492 3.040 nonbonded pdb=" O LEU B 171 " pdb=" OD1 ASN B 172 " model vdw 2.503 3.040 nonbonded pdb=" N PRO I 320 " pdb=" N LEU I 321 " model vdw 2.520 2.560 nonbonded pdb=" O GLN B 244 " pdb=" OE1 GLN B 244 " model vdw 2.524 3.040 ... (remaining 231693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 254 or resid 268 through 305)) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 8 through 351) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 136 or resid 152 through 270 or resid 296 throug \ h 445)) selection = (chain 'F' and (resid 1 through 244 or resid 257 through 445)) } ncs_group { reference = (chain 'G' and resid 177 through 518) selection = (chain 'H' and resid 177 through 518) } ncs_group { reference = (chain 'I' and (resid 39 through 456 or resid 481 through 499)) selection = (chain 'J' and resid 39 through 499) } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 29.480 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31863 Z= 0.129 Angle : 0.603 12.688 43138 Z= 0.312 Chirality : 0.044 0.216 5023 Planarity : 0.004 0.133 5520 Dihedral : 15.537 87.683 11925 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.55 % Favored : 94.12 % Rotamer: Outliers : 1.15 % Allowed : 18.00 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3947 helix: 1.98 (0.15), residues: 1358 sheet: -0.35 (0.20), residues: 713 loop : -1.28 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 321 TYR 0.024 0.001 TYR E 94 PHE 0.011 0.001 PHE C 177 TRP 0.035 0.001 TRP E 282 HIS 0.004 0.001 HIS L 114 Details of bonding type rmsd covalent geometry : bond 0.00282 (31860) covalent geometry : angle 0.60224 (43132) SS BOND : bond 0.00326 ( 3) SS BOND : angle 2.15437 ( 6) hydrogen bonds : bond 0.17514 ( 1143) hydrogen bonds : angle 5.53400 ( 3267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: F 3 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: F 50 GLU cc_start: 0.8748 (mm-30) cc_final: 0.7269 (pm20) REVERT: F 71 MET cc_start: 0.8175 (tpt) cc_final: 0.7397 (tpt) REVERT: F 237 PHE cc_start: 0.8409 (m-80) cc_final: 0.8056 (m-80) REVERT: F 238 SER cc_start: 0.5969 (OUTLIER) cc_final: 0.5603 (t) REVERT: K 179 ASN cc_start: 0.8927 (m110) cc_final: 0.8440 (m110) REVERT: J 270 ASP cc_start: 0.9367 (m-30) cc_final: 0.9117 (p0) REVERT: J 324 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8658 (pm20) REVERT: D 314 ASP cc_start: 0.8318 (t0) cc_final: 0.7746 (t0) REVERT: D 347 ASP cc_start: 0.8832 (t0) cc_final: 0.8562 (t0) REVERT: B 104 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8793 (mp) REVERT: G 452 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.5872 (m-80) REVERT: G 517 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7239 (ppt-90) REVERT: A 70 GLU cc_start: 0.9048 (tp30) cc_final: 0.8795 (tp30) REVERT: H 194 GLN cc_start: 0.8491 (mt0) cc_final: 0.8162 (mp10) REVERT: H 452 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.5736 (m-80) outliers start: 40 outliers final: 22 residues processed: 206 average time/residue: 0.1768 time to fit residues: 63.0201 Evaluate side-chains 191 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 155 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 0.0040 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.085585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054963 restraints weight = 101824.592| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.80 r_work: 0.2845 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31863 Z= 0.098 Angle : 0.516 13.546 43138 Z= 0.266 Chirality : 0.043 0.159 5023 Planarity : 0.004 0.104 5520 Dihedral : 5.407 64.233 4391 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.12 % Favored : 94.60 % Rotamer: Outliers : 2.44 % Allowed : 16.60 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3947 helix: 1.96 (0.15), residues: 1419 sheet: -0.33 (0.20), residues: 715 loop : -1.25 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 321 TYR 0.017 0.001 TYR L 142 PHE 0.032 0.001 PHE K 138 TRP 0.019 0.001 TRP E 282 HIS 0.003 0.000 HIS I 337 Details of bonding type rmsd covalent geometry : bond 0.00210 (31860) covalent geometry : angle 0.51619 (43132) SS BOND : bond 0.00339 ( 3) SS BOND : angle 1.27120 ( 6) hydrogen bonds : bond 0.04004 ( 1143) hydrogen bonds : angle 4.20921 ( 3267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 175 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: F 3 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: F 50 GLU cc_start: 0.8724 (mm-30) cc_final: 0.7340 (pm20) REVERT: F 71 MET cc_start: 0.8059 (tpt) cc_final: 0.6557 (tpt) REVERT: F 237 PHE cc_start: 0.8402 (m-80) cc_final: 0.8032 (m-80) REVERT: F 238 SER cc_start: 0.6111 (OUTLIER) cc_final: 0.5750 (t) REVERT: K 179 ASN cc_start: 0.8950 (m110) cc_final: 0.8524 (m-40) REVERT: D 314 ASP cc_start: 0.8284 (t0) cc_final: 0.7792 (t0) REVERT: D 347 ASP cc_start: 0.8796 (t0) cc_final: 0.8532 (t0) REVERT: B 104 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8908 (mp) REVERT: G 246 GLU cc_start: 0.8104 (tp30) cc_final: 0.7891 (tp30) REVERT: G 423 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8590 (mp) REVERT: G 452 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: E 16 MET cc_start: 0.7803 (mpp) cc_final: 0.7398 (mpp) REVERT: E 69 MET cc_start: 0.6605 (pmm) cc_final: 0.5870 (pmm) REVERT: E 393 MET cc_start: 0.8513 (pmm) cc_final: 0.8203 (pmm) REVERT: I 260 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 70 GLU cc_start: 0.9064 (tp30) cc_final: 0.8824 (tp30) REVERT: A 76 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8681 (tp) REVERT: A 78 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8062 (mm) REVERT: H 495 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: L 60 ASN cc_start: 0.9117 (t0) cc_final: 0.8810 (t0) REVERT: L 106 LYS cc_start: 0.9309 (pptt) cc_final: 0.8866 (tppt) outliers start: 85 outliers final: 38 residues processed: 249 average time/residue: 0.1793 time to fit residues: 77.0153 Evaluate side-chains 212 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 437 CYS Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain H residue 495 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 155 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 106 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 288 optimal weight: 0.8980 chunk 365 optimal weight: 4.9990 chunk 291 optimal weight: 0.1980 chunk 44 optimal weight: 0.0040 chunk 218 optimal weight: 0.4980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.085929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.055478 restraints weight = 102360.545| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.74 r_work: 0.2860 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31863 Z= 0.090 Angle : 0.490 10.544 43138 Z= 0.252 Chirality : 0.043 0.161 5023 Planarity : 0.004 0.105 5520 Dihedral : 5.027 63.023 4371 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.84 % Favored : 94.86 % Rotamer: Outliers : 2.26 % Allowed : 16.48 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3947 helix: 1.96 (0.15), residues: 1431 sheet: -0.15 (0.21), residues: 693 loop : -1.21 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 321 TYR 0.018 0.001 TYR L 142 PHE 0.046 0.001 PHE K 138 TRP 0.022 0.001 TRP E 282 HIS 0.003 0.000 HIS I 337 Details of bonding type rmsd covalent geometry : bond 0.00191 (31860) covalent geometry : angle 0.48982 (43132) SS BOND : bond 0.00346 ( 3) SS BOND : angle 1.40003 ( 6) hydrogen bonds : bond 0.03323 ( 1143) hydrogen bonds : angle 3.91569 ( 3267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 179 time to evaluate : 1.138 Fit side-chains REVERT: F 3 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: F 50 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7093 (pm20) REVERT: F 71 MET cc_start: 0.7927 (tpt) cc_final: 0.5834 (tpt) REVERT: F 237 PHE cc_start: 0.8329 (m-80) cc_final: 0.8018 (m-80) REVERT: K 179 ASN cc_start: 0.8895 (m110) cc_final: 0.8500 (m-40) REVERT: D 314 ASP cc_start: 0.8273 (t70) cc_final: 0.7793 (t0) REVERT: D 347 ASP cc_start: 0.8790 (t0) cc_final: 0.8572 (t0) REVERT: B 104 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8912 (mp) REVERT: G 246 GLU cc_start: 0.8197 (tp30) cc_final: 0.7169 (tm-30) REVERT: G 423 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8516 (mp) REVERT: G 452 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.5850 (m-80) REVERT: E 16 MET cc_start: 0.7724 (mpp) cc_final: 0.7392 (mpp) REVERT: E 69 MET cc_start: 0.6744 (pmm) cc_final: 0.6249 (pmm) REVERT: E 84 MET cc_start: 0.7080 (tmt) cc_final: 0.6728 (tmt) REVERT: E 393 MET cc_start: 0.8621 (pmm) cc_final: 0.8310 (pmm) REVERT: I 260 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7918 (t80) REVERT: C 203 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8293 (tpt) REVERT: A 70 GLU cc_start: 0.9047 (tp30) cc_final: 0.8802 (tp30) REVERT: A 76 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8620 (tp) REVERT: A 78 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7935 (mm) REVERT: H 207 MET cc_start: 0.7308 (ttp) cc_final: 0.7070 (ttp) REVERT: H 495 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: L 60 ASN cc_start: 0.9141 (t0) cc_final: 0.8856 (t0) REVERT: L 106 LYS cc_start: 0.9335 (pptt) cc_final: 0.8894 (tppt) outliers start: 79 outliers final: 44 residues processed: 247 average time/residue: 0.1758 time to fit residues: 75.1627 Evaluate side-chains 221 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain K residue 142 TYR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 495 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 155 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 217 optimal weight: 0.0370 chunk 301 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 357 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 289 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 192 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.086360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056060 restraints weight = 102257.028| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.74 r_work: 0.2874 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31863 Z= 0.086 Angle : 0.485 15.563 43138 Z= 0.249 Chirality : 0.043 0.160 5023 Planarity : 0.004 0.106 5520 Dihedral : 4.849 61.828 4369 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.92 % Favored : 94.78 % Rotamer: Outliers : 2.24 % Allowed : 16.97 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3947 helix: 2.05 (0.15), residues: 1431 sheet: -0.05 (0.21), residues: 691 loop : -1.18 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 321 TYR 0.018 0.001 TYR L 142 PHE 0.063 0.001 PHE K 138 TRP 0.025 0.001 TRP E 282 HIS 0.003 0.000 HIS I 337 Details of bonding type rmsd covalent geometry : bond 0.00183 (31860) covalent geometry : angle 0.48490 (43132) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.33284 ( 6) hydrogen bonds : bond 0.02954 ( 1143) hydrogen bonds : angle 3.73400 ( 3267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: F 3 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: F 50 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7228 (pm20) REVERT: F 71 MET cc_start: 0.7876 (tpt) cc_final: 0.7002 (tpt) REVERT: F 237 PHE cc_start: 0.8329 (m-80) cc_final: 0.7934 (m-80) REVERT: F 238 SER cc_start: 0.6470 (OUTLIER) cc_final: 0.5988 (t) REVERT: F 261 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7308 (tt) REVERT: F 305 MET cc_start: 0.8098 (pmm) cc_final: 0.7523 (pmm) REVERT: K 179 ASN cc_start: 0.8910 (m110) cc_final: 0.8490 (m-40) REVERT: D 314 ASP cc_start: 0.8237 (t70) cc_final: 0.7770 (t0) REVERT: G 246 GLU cc_start: 0.8103 (tp30) cc_final: 0.7193 (tm-30) REVERT: G 452 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.5836 (m-80) REVERT: E 16 MET cc_start: 0.7675 (mpp) cc_final: 0.7314 (mpp) REVERT: E 69 MET cc_start: 0.6889 (pmm) cc_final: 0.6140 (pmm) REVERT: E 84 MET cc_start: 0.7329 (tmt) cc_final: 0.6796 (tmt) REVERT: E 393 MET cc_start: 0.8647 (pmm) cc_final: 0.8339 (pmm) REVERT: I 260 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8005 (t80) REVERT: I 498 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8717 (tptt) REVERT: C 203 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8242 (tpt) REVERT: A 70 GLU cc_start: 0.9036 (tp30) cc_final: 0.8787 (tp30) REVERT: A 76 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (tp) REVERT: H 495 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8628 (mp0) REVERT: L 106 LYS cc_start: 0.9320 (pptt) cc_final: 0.8865 (tppt) outliers start: 78 outliers final: 43 residues processed: 248 average time/residue: 0.1750 time to fit residues: 75.0963 Evaluate side-chains 221 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 416 GLU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 142 TYR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 436 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 498 LYS Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 495 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 155 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 56 optimal weight: 7.9990 chunk 381 optimal weight: 0.0670 chunk 191 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 38 optimal weight: 30.0000 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 304 HIS J 376 ASN E 41 ASN E 350 HIS ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.083217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.052457 restraints weight = 103099.860| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.74 r_work: 0.2776 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 31863 Z= 0.211 Angle : 0.595 12.711 43138 Z= 0.309 Chirality : 0.045 0.160 5023 Planarity : 0.005 0.127 5520 Dihedral : 5.054 62.072 4361 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.98 % Favored : 93.69 % Rotamer: Outliers : 2.44 % Allowed : 17.37 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3947 helix: 1.93 (0.14), residues: 1424 sheet: -0.32 (0.21), residues: 652 loop : -1.28 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 289 TYR 0.020 0.001 TYR L 142 PHE 0.065 0.002 PHE K 138 TRP 0.031 0.002 TRP E 282 HIS 0.007 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00507 (31860) covalent geometry : angle 0.59436 (43132) SS BOND : bond 0.01044 ( 3) SS BOND : angle 1.86353 ( 6) hydrogen bonds : bond 0.05382 ( 1143) hydrogen bonds : angle 4.18003 ( 3267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 162 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: F 3 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: F 71 MET cc_start: 0.7947 (tpt) cc_final: 0.6478 (tpt) REVERT: F 237 PHE cc_start: 0.8516 (m-80) cc_final: 0.8126 (m-80) REVERT: F 238 SER cc_start: 0.6539 (OUTLIER) cc_final: 0.6101 (t) REVERT: F 261 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7492 (tt) REVERT: F 305 MET cc_start: 0.8036 (pmm) cc_final: 0.7715 (pmm) REVERT: K 106 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9096 (tppt) REVERT: K 179 ASN cc_start: 0.8950 (m110) cc_final: 0.8569 (m-40) REVERT: D 314 ASP cc_start: 0.8464 (t70) cc_final: 0.7982 (t0) REVERT: B 104 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8846 (mp) REVERT: B 244 GLN cc_start: 0.9348 (tp40) cc_final: 0.8783 (tp-100) REVERT: G 246 GLU cc_start: 0.8275 (tp30) cc_final: 0.8036 (tp30) REVERT: G 423 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8571 (mp) REVERT: G 452 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5934 (m-80) REVERT: G 517 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7128 (ppt-90) REVERT: E 69 MET cc_start: 0.7044 (pmm) cc_final: 0.6819 (pmm) REVERT: E 393 MET cc_start: 0.8601 (pmm) cc_final: 0.8193 (pmm) REVERT: C 203 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8445 (tpt) REVERT: A 76 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8754 (tp) REVERT: H 452 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: L 19 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8145 (t) REVERT: L 30 MET cc_start: 0.6906 (tpt) cc_final: 0.6653 (tpt) REVERT: L 106 LYS cc_start: 0.9362 (pptt) cc_final: 0.8912 (tppt) outliers start: 85 outliers final: 48 residues processed: 237 average time/residue: 0.1759 time to fit residues: 72.1870 Evaluate side-chains 219 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain K residue 142 TYR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 437 CYS Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain H residue 196 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 142 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 163 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 222 optimal weight: 0.0010 chunk 129 optimal weight: 0.2980 chunk 264 optimal weight: 4.9990 chunk 251 optimal weight: 0.5980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.053160 restraints weight = 100962.129| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.84 r_work: 0.2810 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31863 Z= 0.113 Angle : 0.521 12.128 43138 Z= 0.267 Chirality : 0.043 0.163 5023 Planarity : 0.004 0.115 5520 Dihedral : 4.839 62.730 4359 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.14 % Favored : 94.55 % Rotamer: Outliers : 2.12 % Allowed : 17.74 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3947 helix: 2.00 (0.15), residues: 1430 sheet: -0.17 (0.21), residues: 631 loop : -1.28 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 29 TYR 0.020 0.001 TYR E 94 PHE 0.055 0.001 PHE K 138 TRP 0.031 0.001 TRP E 282 HIS 0.003 0.000 HIS I 337 Details of bonding type rmsd covalent geometry : bond 0.00261 (31860) covalent geometry : angle 0.52017 (43132) SS BOND : bond 0.00919 ( 3) SS BOND : angle 1.70770 ( 6) hydrogen bonds : bond 0.03800 ( 1143) hydrogen bonds : angle 3.87256 ( 3267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 167 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: F 3 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: F 50 GLU cc_start: 0.8725 (mm-30) cc_final: 0.6932 (pm20) REVERT: F 71 MET cc_start: 0.7938 (tpt) cc_final: 0.5115 (tpt) REVERT: F 237 PHE cc_start: 0.8440 (m-80) cc_final: 0.8028 (m-80) REVERT: F 238 SER cc_start: 0.6662 (OUTLIER) cc_final: 0.6167 (t) REVERT: K 53 ARG cc_start: 0.8638 (pmt170) cc_final: 0.8064 (pmt170) REVERT: K 179 ASN cc_start: 0.8934 (m110) cc_final: 0.8565 (m-40) REVERT: D 72 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: D 314 ASP cc_start: 0.8380 (t70) cc_final: 0.7941 (t0) REVERT: B 104 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8768 (mp) REVERT: B 244 GLN cc_start: 0.9339 (tp40) cc_final: 0.9062 (tp-100) REVERT: G 246 GLU cc_start: 0.8244 (tp30) cc_final: 0.7983 (tp30) REVERT: G 423 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8538 (mp) REVERT: G 452 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.5855 (m-80) REVERT: E 16 MET cc_start: 0.7761 (mpp) cc_final: 0.7442 (mpp) REVERT: E 69 MET cc_start: 0.7236 (pmm) cc_final: 0.7033 (pmm) REVERT: E 393 MET cc_start: 0.8600 (pmm) cc_final: 0.8160 (pmm) REVERT: I 260 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7825 (t80) REVERT: I 498 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8728 (tptt) REVERT: C 203 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8385 (tpt) REVERT: A 76 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8640 (tp) REVERT: H 194 GLN cc_start: 0.8367 (mt0) cc_final: 0.7994 (mp10) REVERT: H 452 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: L 19 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8187 (t) REVERT: L 30 MET cc_start: 0.6945 (tpt) cc_final: 0.6646 (tpp) REVERT: L 106 LYS cc_start: 0.9356 (pptt) cc_final: 0.8905 (tppt) outliers start: 74 outliers final: 47 residues processed: 228 average time/residue: 0.1725 time to fit residues: 68.6815 Evaluate side-chains 222 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 416 GLU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 142 TYR Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 437 CYS Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 498 ASP Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 498 LYS Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain H residue 196 MET Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 155 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 227 optimal weight: 0.0020 chunk 5 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 277 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 268 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 301 optimal weight: 0.9980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054506 restraints weight = 102157.685| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.72 r_work: 0.2832 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31863 Z= 0.101 Angle : 0.517 11.138 43138 Z= 0.263 Chirality : 0.043 0.178 5023 Planarity : 0.004 0.117 5520 Dihedral : 4.701 62.822 4357 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.40 % Favored : 94.32 % Rotamer: Outliers : 2.15 % Allowed : 17.74 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3947 helix: 2.08 (0.15), residues: 1430 sheet: -0.16 (0.21), residues: 656 loop : -1.26 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.021 0.001 TYR E 94 PHE 0.047 0.001 PHE K 138 TRP 0.032 0.001 TRP E 282 HIS 0.003 0.000 HIS I 337 Details of bonding type rmsd covalent geometry : bond 0.00230 (31860) covalent geometry : angle 0.51652 (43132) SS BOND : bond 0.00421 ( 3) SS BOND : angle 1.50700 ( 6) hydrogen bonds : bond 0.03419 ( 1143) hydrogen bonds : angle 3.74285 ( 3267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 165 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: F 50 GLU cc_start: 0.8608 (mm-30) cc_final: 0.6861 (pm20) REVERT: F 71 MET cc_start: 0.8065 (tpt) cc_final: 0.6176 (tpt) REVERT: F 237 PHE cc_start: 0.8404 (m-80) cc_final: 0.7981 (m-80) REVERT: F 238 SER cc_start: 0.6557 (OUTLIER) cc_final: 0.6050 (t) REVERT: F 266 PHE cc_start: 0.8977 (t80) cc_final: 0.8756 (m-80) REVERT: F 393 MET cc_start: 0.4700 (ppp) cc_final: 0.4342 (ppp) REVERT: K 106 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9083 (tppt) REVERT: K 179 ASN cc_start: 0.8936 (m110) cc_final: 0.8526 (m-40) REVERT: D 72 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: D 314 ASP cc_start: 0.8353 (t70) cc_final: 0.7935 (t0) REVERT: B 104 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8837 (mp) REVERT: B 244 GLN cc_start: 0.9334 (tp40) cc_final: 0.9044 (tp-100) REVERT: G 246 GLU cc_start: 0.8276 (tp30) cc_final: 0.8007 (tp30) REVERT: G 423 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8508 (mp) REVERT: G 452 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.5866 (m-80) REVERT: G 517 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7154 (ppt-90) REVERT: E 16 MET cc_start: 0.7771 (mpp) cc_final: 0.7358 (mpp) REVERT: E 69 MET cc_start: 0.7418 (pmm) cc_final: 0.7174 (pmm) REVERT: E 393 MET cc_start: 0.8645 (pmm) cc_final: 0.8245 (pmm) REVERT: I 498 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8717 (tptt) REVERT: C 203 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8356 (tpt) REVERT: A 76 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8584 (tp) REVERT: H 194 GLN cc_start: 0.8372 (mt0) cc_final: 0.7983 (mp10) REVERT: H 452 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6073 (m-80) REVERT: L 19 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8182 (t) REVERT: L 30 MET cc_start: 0.7084 (tpt) cc_final: 0.6874 (tpp) REVERT: L 68 ASN cc_start: 0.8723 (m-40) cc_final: 0.8504 (m110) REVERT: L 106 LYS cc_start: 0.9350 (pptt) cc_final: 0.8899 (tppt) outliers start: 75 outliers final: 49 residues processed: 229 average time/residue: 0.1739 time to fit residues: 69.0828 Evaluate side-chains 224 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 416 GLU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 437 CYS Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 498 LYS Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain H residue 196 MET Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 142 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 376 optimal weight: 0.0020 chunk 183 optimal weight: 0.6980 chunk 384 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 371 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.085821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055388 restraints weight = 102298.137| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.75 r_work: 0.2854 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31863 Z= 0.089 Angle : 0.504 13.039 43138 Z= 0.255 Chirality : 0.043 0.161 5023 Planarity : 0.004 0.117 5520 Dihedral : 4.528 62.172 4355 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.99 % Favored : 94.76 % Rotamer: Outliers : 1.92 % Allowed : 18.06 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3947 helix: 2.16 (0.15), residues: 1424 sheet: -0.10 (0.21), residues: 689 loop : -1.19 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.021 0.001 TYR E 94 PHE 0.042 0.001 PHE K 138 TRP 0.036 0.001 TRP E 282 HIS 0.003 0.000 HIS I 337 Details of bonding type rmsd covalent geometry : bond 0.00196 (31860) covalent geometry : angle 0.50413 (43132) SS BOND : bond 0.00359 ( 3) SS BOND : angle 1.51737 ( 6) hydrogen bonds : bond 0.02947 ( 1143) hydrogen bonds : angle 3.62879 ( 3267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 3 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: F 50 GLU cc_start: 0.8521 (mm-30) cc_final: 0.6872 (pm20) REVERT: F 71 MET cc_start: 0.7926 (tpt) cc_final: 0.6001 (tpt) REVERT: F 237 PHE cc_start: 0.8400 (m-80) cc_final: 0.8014 (m-80) REVERT: F 238 SER cc_start: 0.6503 (OUTLIER) cc_final: 0.6023 (t) REVERT: F 393 MET cc_start: 0.4581 (ppp) cc_final: 0.4239 (ppp) REVERT: K 53 ARG cc_start: 0.8540 (pmt170) cc_final: 0.7910 (pmt170) REVERT: K 179 ASN cc_start: 0.8918 (m110) cc_final: 0.8514 (m-40) REVERT: D 72 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: D 314 ASP cc_start: 0.8274 (t70) cc_final: 0.7854 (t0) REVERT: B 104 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 244 GLN cc_start: 0.9336 (tp40) cc_final: 0.9043 (tp-100) REVERT: G 246 GLU cc_start: 0.8223 (tp30) cc_final: 0.7377 (tm-30) REVERT: G 423 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8473 (mp) REVERT: G 452 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5846 (m-80) REVERT: G 517 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7053 (ppt-90) REVERT: E 16 MET cc_start: 0.7862 (mpp) cc_final: 0.7541 (mpp) REVERT: E 69 MET cc_start: 0.7482 (pmm) cc_final: 0.7252 (pmm) REVERT: E 393 MET cc_start: 0.8659 (pmm) cc_final: 0.8334 (pmm) REVERT: I 498 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8717 (tptt) REVERT: C 203 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8299 (tpt) REVERT: A 76 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8500 (tp) REVERT: H 495 GLU cc_start: 0.8953 (mp0) cc_final: 0.8728 (mp0) REVERT: L 19 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8179 (t) REVERT: L 30 MET cc_start: 0.6926 (tpt) cc_final: 0.6724 (tpp) REVERT: L 106 LYS cc_start: 0.9322 (pptt) cc_final: 0.8836 (tppt) outliers start: 67 outliers final: 44 residues processed: 228 average time/residue: 0.1731 time to fit residues: 68.8735 Evaluate side-chains 220 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 416 GLU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 498 LYS Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain H residue 196 MET Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 270 optimal weight: 3.9990 chunk 383 optimal weight: 0.0020 chunk 323 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 299 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 63 optimal weight: 0.0870 chunk 302 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.086351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055974 restraints weight = 101995.430| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.76 r_work: 0.2870 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31863 Z= 0.086 Angle : 0.508 15.812 43138 Z= 0.254 Chirality : 0.043 0.161 5023 Planarity : 0.004 0.118 5520 Dihedral : 4.452 61.180 4354 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.76 % Favored : 94.98 % Rotamer: Outliers : 1.78 % Allowed : 18.23 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3947 helix: 2.17 (0.15), residues: 1429 sheet: 0.03 (0.21), residues: 703 loop : -1.15 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.020 0.001 TYR E 94 PHE 0.041 0.001 PHE K 138 TRP 0.034 0.001 TRP E 282 HIS 0.003 0.000 HIS I 337 Details of bonding type rmsd covalent geometry : bond 0.00184 (31860) covalent geometry : angle 0.50750 (43132) SS BOND : bond 0.00380 ( 3) SS BOND : angle 1.39971 ( 6) hydrogen bonds : bond 0.02712 ( 1143) hydrogen bonds : angle 3.56439 ( 3267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 3 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: F 50 GLU cc_start: 0.8471 (mm-30) cc_final: 0.6932 (pm20) REVERT: F 71 MET cc_start: 0.7955 (tpt) cc_final: 0.6050 (tpt) REVERT: F 237 PHE cc_start: 0.8360 (m-80) cc_final: 0.7979 (m-80) REVERT: F 238 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6203 (t) REVERT: K 53 ARG cc_start: 0.8451 (pmt170) cc_final: 0.7780 (pmt170) REVERT: K 179 ASN cc_start: 0.8922 (m110) cc_final: 0.8524 (m-40) REVERT: J 324 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: D 314 ASP cc_start: 0.8259 (t70) cc_final: 0.7844 (t0) REVERT: B 104 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8812 (mp) REVERT: B 244 GLN cc_start: 0.9324 (tp40) cc_final: 0.9027 (tp-100) REVERT: G 246 GLU cc_start: 0.8159 (tp30) cc_final: 0.7312 (tm-30) REVERT: G 423 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8433 (mp) REVERT: G 452 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: G 517 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7059 (ppt-90) REVERT: E 16 MET cc_start: 0.7678 (mpp) cc_final: 0.7346 (mpp) REVERT: E 69 MET cc_start: 0.7476 (pmm) cc_final: 0.7252 (pmm) REVERT: E 393 MET cc_start: 0.8661 (pmm) cc_final: 0.8337 (pmm) REVERT: I 498 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8711 (tptt) REVERT: C 203 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8339 (tpt) REVERT: A 76 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 210 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9336 (tp) REVERT: H 495 GLU cc_start: 0.8909 (mp0) cc_final: 0.8690 (mp0) REVERT: L 19 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8264 (t) REVERT: L 30 MET cc_start: 0.6891 (tpt) cc_final: 0.6676 (tpp) REVERT: L 106 LYS cc_start: 0.9338 (pptt) cc_final: 0.8926 (tppt) outliers start: 62 outliers final: 42 residues processed: 223 average time/residue: 0.1679 time to fit residues: 65.2338 Evaluate side-chains 220 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 416 GLU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 498 LYS Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain H residue 196 MET Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 359 optimal weight: 4.9990 chunk 360 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 328 optimal weight: 0.5980 chunk 391 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 370 optimal weight: 7.9990 chunk 125 optimal weight: 0.0570 chunk 191 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.086208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.055861 restraints weight = 101861.243| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.73 r_work: 0.2867 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31863 Z= 0.089 Angle : 0.506 15.260 43138 Z= 0.254 Chirality : 0.043 0.176 5023 Planarity : 0.004 0.122 5520 Dihedral : 4.395 60.434 4354 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.71 % Favored : 95.03 % Rotamer: Outliers : 1.78 % Allowed : 18.14 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3947 helix: 2.21 (0.15), residues: 1426 sheet: 0.10 (0.21), residues: 697 loop : -1.12 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.021 0.001 TYR E 94 PHE 0.039 0.001 PHE K 138 TRP 0.036 0.001 TRP E 282 HIS 0.012 0.000 HIS L 114 Details of bonding type rmsd covalent geometry : bond 0.00197 (31860) covalent geometry : angle 0.50602 (43132) SS BOND : bond 0.00351 ( 3) SS BOND : angle 1.39059 ( 6) hydrogen bonds : bond 0.02853 ( 1143) hydrogen bonds : angle 3.56346 ( 3267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: F 3 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: F 50 GLU cc_start: 0.8457 (mm-30) cc_final: 0.6919 (pm20) REVERT: F 71 MET cc_start: 0.7959 (tpt) cc_final: 0.6052 (tpt) REVERT: F 237 PHE cc_start: 0.8346 (m-80) cc_final: 0.7959 (m-80) REVERT: F 238 SER cc_start: 0.6718 (OUTLIER) cc_final: 0.6231 (t) REVERT: K 53 ARG cc_start: 0.8444 (pmt170) cc_final: 0.7797 (pmt170) REVERT: K 106 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9046 (tppt) REVERT: K 179 ASN cc_start: 0.8920 (m110) cc_final: 0.8529 (m-40) REVERT: J 324 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: D 314 ASP cc_start: 0.8291 (t70) cc_final: 0.7923 (t0) REVERT: B 104 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8829 (mp) REVERT: B 244 GLN cc_start: 0.9323 (tp40) cc_final: 0.9028 (tp-100) REVERT: G 246 GLU cc_start: 0.8158 (tp30) cc_final: 0.7321 (tm-30) REVERT: G 423 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8433 (mp) REVERT: G 452 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.5827 (m-80) REVERT: G 517 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7128 (ppt-90) REVERT: E 16 MET cc_start: 0.7565 (mpp) cc_final: 0.7225 (mpp) REVERT: E 69 MET cc_start: 0.7384 (pmm) cc_final: 0.7157 (pmm) REVERT: E 393 MET cc_start: 0.8661 (pmm) cc_final: 0.8360 (pmm) REVERT: I 498 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8728 (tptt) REVERT: C 203 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8298 (tpt) REVERT: A 76 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8463 (tp) REVERT: A 210 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9344 (tp) REVERT: H 452 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.5974 (m-80) REVERT: H 495 GLU cc_start: 0.8901 (mp0) cc_final: 0.8681 (mp0) REVERT: L 19 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8185 (t) REVERT: L 30 MET cc_start: 0.6829 (tpt) cc_final: 0.6621 (tpp) REVERT: L 106 LYS cc_start: 0.9358 (pptt) cc_final: 0.8928 (tppt) outliers start: 62 outliers final: 44 residues processed: 221 average time/residue: 0.1669 time to fit residues: 63.9464 Evaluate side-chains 223 residues out of total 3489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 416 GLU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 106 LYS Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 437 CYS Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 260 PHE Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 498 LYS Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain H residue 196 MET Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 62 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 367 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN L 114 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.084228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053579 restraints weight = 102473.652| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.72 r_work: 0.2806 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31863 Z= 0.151 Angle : 0.553 15.176 43138 Z= 0.282 Chirality : 0.044 0.162 5023 Planarity : 0.004 0.132 5520 Dihedral : 4.671 60.696 4353 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.60 % Favored : 94.10 % Rotamer: Outliers : 1.69 % Allowed : 18.26 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3947 helix: 2.13 (0.15), residues: 1428 sheet: 0.04 (0.22), residues: 622 loop : -1.17 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.022 0.001 TYR E 94 PHE 0.039 0.001 PHE K 138 TRP 0.039 0.001 TRP E 282 HIS 0.010 0.001 HIS L 114 Details of bonding type rmsd covalent geometry : bond 0.00356 (31860) covalent geometry : angle 0.55311 (43132) SS BOND : bond 0.00532 ( 3) SS BOND : angle 1.60715 ( 6) hydrogen bonds : bond 0.04313 ( 1143) hydrogen bonds : angle 3.83857 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9507.20 seconds wall clock time: 163 minutes 2.40 seconds (9782.40 seconds total)