Starting phenix.real_space_refine on Mon Sep 30 02:49:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/09_2024/7xkp_33259.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/09_2024/7xkp_33259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/09_2024/7xkp_33259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/09_2024/7xkp_33259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/09_2024/7xkp_33259.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/09_2024/7xkp_33259.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 77 5.16 5 C 15232 2.51 5 N 4193 2.21 5 O 4600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24105 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 272} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.14, per 1000 atoms: 0.63 Number of scatterers: 24105 At special positions: 0 Unit cell: (128.48, 126.72, 157.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 2 15.00 Mg 1 11.99 O 4600 8.00 N 4193 7.00 C 15232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 3.4 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5710 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 23 sheets defined 48.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.296A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.568A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.882A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 251 Proline residue: A 239 - end of helix removed outlier: 3.599A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.996A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.772A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.769A pdb=" N ALA A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.559A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.608A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.532A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.514A pdb=" N PHE B 350 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 4.134A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 421 removed outlier: 4.716A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 440 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 478 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.550A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.563A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.645A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.877A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.740A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 381 through 400 removed outlier: 4.416A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.690A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 467 removed outlier: 4.362A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.595A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.540A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.670A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.803A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.753A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 385 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.583A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.678A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 4.080A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 5.204A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.711A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.641A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.420A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.568A pdb=" N ARG E 404 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.661A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.970A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.584A pdb=" N LEU F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.637A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 226 removed outlier: 3.556A pdb=" N ARG F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 242 removed outlier: 3.800A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.921A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.556A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.599A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 388 through 392 removed outlier: 3.661A pdb=" N GLU F 391 " --> pdb=" O GLY F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.631A pdb=" N LEU F 398 " --> pdb=" O ASP F 394 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.791A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 3.541A pdb=" N ARG G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 58 removed outlier: 3.631A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.971A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.836A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 284 removed outlier: 3.757A pdb=" N ILE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.746A pdb=" N SER G 261 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.963A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.395A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.746A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLN A 341 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY A 360 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE A 343 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.353A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.915A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.814A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.584A pdb=" N ILE B 159 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.531A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 356 " --> pdb=" O GLN B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.531A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.480A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.292A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 108 removed outlier: 8.839A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 10 removed outlier: 6.720A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.514A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.445A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.933A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.440A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.538A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.303A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 135 through 137 removed outlier: 3.997A pdb=" N LEU G 135 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 117 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N TYR G 175 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) 1154 hydrogen bonds defined for protein. 3303 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: 8.39 Time building geometry restraints manager: 7.24 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: 8203 1.34 - 1.46: 3528 1.46 - 1.57: 12620 1.57 - 1.69: 3 1.69 - 1.81: 154 Bond restraints: 24508 Sorted by residual: bond pdb=" CA ASP C 289 " pdb=" CB ASP C 289 " ideal model delta sigma weight residual 1.532 1.546 -0.015 1.33e-02 5.65e+03 1.22e+00 bond pdb=" CD GLU D 464 " pdb=" OE1 GLU D 464 " ideal model delta sigma weight residual 1.249 1.229 0.020 1.90e-02 2.77e+03 1.14e+00 bond pdb=" CB ASP C 289 " pdb=" CG ASP C 289 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.05e+00 bond pdb=" C4 ADP F 602 " pdb=" C5 ADP F 602 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C ARG G 256 " pdb=" O ARG G 256 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.19e-02 7.06e+03 1.02e+00 ... (remaining 24503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 32758 1.69 - 3.39: 386 3.39 - 5.08: 51 5.08 - 6.78: 7 6.78 - 8.47: 1 Bond angle restraints: 33203 Sorted by residual: angle pdb=" CA GLY B 340 " pdb=" C GLY B 340 " pdb=" N GLN B 341 " ideal model delta sigma weight residual 114.23 117.49 -3.26 8.80e-01 1.29e+00 1.37e+01 angle pdb=" C GLY C 288 " pdb=" N ASP C 289 " pdb=" CA ASP C 289 " ideal model delta sigma weight residual 124.82 130.29 -5.47 1.78e+00 3.16e-01 9.44e+00 angle pdb=" N GLU E 379 " pdb=" CA GLU E 379 " pdb=" CB GLU E 379 " ideal model delta sigma weight residual 110.16 114.58 -4.42 1.48e+00 4.57e-01 8.91e+00 angle pdb=" C VAL F 214 " pdb=" N PHE F 215 " pdb=" CA PHE F 215 " ideal model delta sigma weight residual 122.42 117.89 4.53 1.55e+00 4.16e-01 8.54e+00 angle pdb=" N GLU E 337 " pdb=" CA GLU E 337 " pdb=" CB GLU E 337 " ideal model delta sigma weight residual 110.16 114.39 -4.23 1.48e+00 4.57e-01 8.17e+00 ... (remaining 33198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 14520 29.88 - 59.76: 350 59.76 - 89.63: 46 89.63 - 119.51: 2 119.51 - 149.39: 1 Dihedral angle restraints: 14919 sinusoidal: 5997 harmonic: 8922 Sorted by residual: dihedral pdb=" CA ALA G 108 " pdb=" C ALA G 108 " pdb=" N SER G 109 " pdb=" CA SER G 109 " ideal model delta harmonic sigma weight residual 180.00 145.71 34.29 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" C5' ADP F 602 " pdb=" O5' ADP F 602 " pdb=" PA ADP F 602 " pdb=" O2A ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 89.39 -149.39 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O2A ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PA ADP F 602 " pdb=" PB ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 50.84 -110.84 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2604 0.037 - 0.074: 853 0.074 - 0.111: 289 0.111 - 0.148: 86 0.148 - 0.185: 2 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CB VAL D 463 " pdb=" CA VAL D 463 " pdb=" CG1 VAL D 463 " pdb=" CG2 VAL D 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA GLU D 464 " pdb=" N GLU D 464 " pdb=" C GLU D 464 " pdb=" CB GLU D 464 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA GLU A 459 " pdb=" N GLU A 459 " pdb=" C GLU A 459 " pdb=" CB GLU A 459 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 3831 not shown) Planarity restraints: 4357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS G 65 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO G 66 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO G 66 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 66 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 341 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO D 342 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 342 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 342 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO D 221 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.023 5.00e-02 4.00e+02 ... (remaining 4354 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 209 2.65 - 3.21: 22411 3.21 - 3.78: 35930 3.78 - 4.34: 50864 4.34 - 4.90: 85715 Nonbonded interactions: 195129 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O1B ADP F 602 " model vdw 2.089 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.214 2.170 nonbonded pdb=" O LEU B 402 " pdb=" OG1 THR B 406 " model vdw 2.240 3.040 nonbonded pdb=" OE1 GLN G 50 " pdb=" OH TYR G 220 " model vdw 2.251 3.040 nonbonded pdb=" NH2 ARG A 106 " pdb=" O GLY A 119 " model vdw 2.265 3.120 ... (remaining 195124 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 54.630 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 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 : 0.002 0.038 24508 Z= 0.162 Angle : 0.479 8.472 33203 Z= 0.259 Chirality : 0.043 0.185 3834 Planarity : 0.004 0.047 4357 Dihedral : 13.187 149.390 9209 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3114 helix: 2.17 (0.15), residues: 1254 sheet: 0.89 (0.23), residues: 524 loop : 0.18 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.006 0.001 TYR E 341 ARG 0.004 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 3.132 Fit side-chains revert: symmetry clash REVERT: G 131 MET cc_start: 0.6235 (mmp) cc_final: 0.5952 (mtp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 1.7352 time to fit residues: 221.5222 Evaluate side-chains 87 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 189 GLN C 474 HIS F 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 24508 Z= 0.616 Angle : 0.689 8.741 33203 Z= 0.362 Chirality : 0.052 0.223 3834 Planarity : 0.005 0.052 4357 Dihedral : 5.937 148.896 3409 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 0.62 % Allowed : 5.88 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3114 helix: 1.60 (0.15), residues: 1243 sheet: 0.49 (0.22), residues: 538 loop : -0.19 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 363 PHE 0.024 0.002 PHE B 494 TYR 0.016 0.002 TYR E 341 ARG 0.006 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 3.079 Fit side-chains revert: symmetry clash REVERT: G 131 MET cc_start: 0.6502 (mmp) cc_final: 0.6131 (mmt) outliers start: 16 outliers final: 5 residues processed: 94 average time/residue: 1.6462 time to fit residues: 177.6352 Evaluate side-chains 89 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 234 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 226 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN B 345 GLN C 185 ASN C 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24508 Z= 0.163 Angle : 0.481 8.698 33203 Z= 0.251 Chirality : 0.043 0.147 3834 Planarity : 0.004 0.044 4357 Dihedral : 5.355 138.598 3409 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.88 % Rotamer: Outliers : 0.90 % Allowed : 7.09 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3114 helix: 2.05 (0.15), residues: 1243 sheet: 0.67 (0.22), residues: 531 loop : 0.04 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.017 0.001 PHE B 494 TYR 0.008 0.001 TYR D 199 ARG 0.003 0.000 ARG E 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 3.330 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9119 (m) REVERT: D 389 MET cc_start: 0.7327 (mpt) cc_final: 0.6923 (mpt) REVERT: D 464 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: F 202 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8325 (mtt) REVERT: G 131 MET cc_start: 0.6429 (mmp) cc_final: 0.6032 (mmt) outliers start: 23 outliers final: 7 residues processed: 104 average time/residue: 1.5889 time to fit residues: 189.6972 Evaluate side-chains 95 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 24508 Z= 0.596 Angle : 0.659 8.189 33203 Z= 0.346 Chirality : 0.051 0.242 3834 Planarity : 0.005 0.053 4357 Dihedral : 5.772 135.463 3409 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 1.44 % Allowed : 8.34 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3114 helix: 1.56 (0.15), residues: 1251 sheet: 0.44 (0.22), residues: 540 loop : -0.30 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 363 PHE 0.022 0.002 PHE B 494 TYR 0.017 0.002 TYR E 341 ARG 0.005 0.001 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 87 time to evaluate : 2.850 Fit side-chains revert: symmetry clash REVERT: B 176 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8838 (m) REVERT: B 487 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9148 (tt) REVERT: F 202 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8174 (mtt) REVERT: G 131 MET cc_start: 0.6500 (mmp) cc_final: 0.6168 (mmt) outliers start: 37 outliers final: 19 residues processed: 116 average time/residue: 1.3074 time to fit residues: 178.1501 Evaluate side-chains 108 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 255 optimal weight: 0.3980 chunk 207 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24508 Z= 0.206 Angle : 0.501 8.967 33203 Z= 0.261 Chirality : 0.044 0.166 3834 Planarity : 0.004 0.048 4357 Dihedral : 5.374 150.615 3409 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.46 % Rotamer: Outliers : 1.05 % Allowed : 9.58 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3114 helix: 1.90 (0.15), residues: 1246 sheet: 0.54 (0.23), residues: 531 loop : -0.12 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.010 0.001 TYR E 341 ARG 0.002 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: F 202 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8343 (mtt) REVERT: G 131 MET cc_start: 0.6535 (mmp) cc_final: 0.6158 (mmt) outliers start: 27 outliers final: 15 residues processed: 109 average time/residue: 1.5212 time to fit residues: 192.0227 Evaluate side-chains 102 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 0.0010 chunk 73 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24508 Z= 0.228 Angle : 0.501 9.758 33203 Z= 0.260 Chirality : 0.044 0.167 3834 Planarity : 0.004 0.048 4357 Dihedral : 5.294 162.334 3409 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.40 % Allowed : 9.89 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.15), residues: 3114 helix: 1.98 (0.15), residues: 1252 sheet: 0.58 (0.23), residues: 531 loop : -0.06 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.016 0.001 PHE B 494 TYR 0.009 0.001 TYR E 341 ARG 0.002 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: B 478 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7809 (p) REVERT: F 202 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8241 (mtt) REVERT: G 131 MET cc_start: 0.6532 (mmp) cc_final: 0.6155 (mmt) outliers start: 36 outliers final: 20 residues processed: 116 average time/residue: 1.4657 time to fit residues: 197.0645 Evaluate side-chains 107 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24508 Z= 0.356 Angle : 0.555 10.511 33203 Z= 0.289 Chirality : 0.046 0.195 3834 Planarity : 0.004 0.050 4357 Dihedral : 5.427 166.236 3409 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.25 % Allowed : 10.36 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3114 helix: 1.85 (0.15), residues: 1251 sheet: 0.50 (0.23), residues: 531 loop : -0.19 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.018 0.001 PHE B 494 TYR 0.013 0.001 TYR E 341 ARG 0.004 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: B 478 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7785 (p) REVERT: D 389 MET cc_start: 0.6870 (mpt) cc_final: 0.6593 (mpp) REVERT: F 202 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8239 (mtt) REVERT: G 131 MET cc_start: 0.6487 (mmp) cc_final: 0.6226 (mmt) outliers start: 32 outliers final: 27 residues processed: 112 average time/residue: 1.4281 time to fit residues: 186.4503 Evaluate side-chains 114 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24508 Z= 0.300 Angle : 0.531 11.031 33203 Z= 0.276 Chirality : 0.045 0.182 3834 Planarity : 0.004 0.049 4357 Dihedral : 5.265 164.624 3409 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.40 % Allowed : 10.67 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3114 helix: 1.88 (0.15), residues: 1251 sheet: 0.50 (0.23), residues: 531 loop : -0.18 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.012 0.001 TYR E 341 ARG 0.003 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 85 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: B 478 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7763 (p) REVERT: D 389 MET cc_start: 0.6887 (mpt) cc_final: 0.6672 (mpp) REVERT: F 202 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8217 (mtt) REVERT: G 131 MET cc_start: 0.6546 (mmp) cc_final: 0.6281 (mmt) outliers start: 36 outliers final: 24 residues processed: 116 average time/residue: 1.3382 time to fit residues: 181.5778 Evaluate side-chains 111 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 24508 Z= 0.532 Angle : 0.634 11.702 33203 Z= 0.330 Chirality : 0.049 0.221 3834 Planarity : 0.005 0.051 4357 Dihedral : 5.514 166.181 3409 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 1.40 % Allowed : 10.91 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3114 helix: 1.60 (0.15), residues: 1249 sheet: 0.34 (0.23), residues: 540 loop : -0.37 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 363 PHE 0.020 0.002 PHE B 494 TYR 0.018 0.001 TYR E 341 ARG 0.004 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: A 489 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8200 (mmtt) REVERT: D 389 MET cc_start: 0.7023 (mpt) cc_final: 0.6703 (tpp) REVERT: F 202 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8242 (mtt) REVERT: G 131 MET cc_start: 0.6514 (mmp) cc_final: 0.6250 (mtp) outliers start: 36 outliers final: 25 residues processed: 119 average time/residue: 1.3712 time to fit residues: 190.2636 Evaluate side-chains 113 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 179 optimal weight: 0.0980 chunk 139 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 245 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24508 Z= 0.185 Angle : 0.511 12.488 33203 Z= 0.262 Chirality : 0.044 0.170 3834 Planarity : 0.004 0.046 4357 Dihedral : 5.170 165.122 3409 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 1.13 % Allowed : 11.22 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3114 helix: 1.93 (0.15), residues: 1251 sheet: 0.46 (0.23), residues: 531 loop : -0.16 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.016 0.001 PHE B 494 TYR 0.009 0.001 TYR E 341 ARG 0.002 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: B 478 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7755 (p) REVERT: F 202 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8328 (mtt) REVERT: G 131 MET cc_start: 0.6510 (mmp) cc_final: 0.6253 (mtp) outliers start: 29 outliers final: 21 residues processed: 113 average time/residue: 1.3962 time to fit residues: 183.4813 Evaluate side-chains 110 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 246 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.060471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.044263 restraints weight = 70543.914| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.80 r_work: 0.2592 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24508 Z= 0.282 Angle : 0.538 12.554 33203 Z= 0.276 Chirality : 0.045 0.177 3834 Planarity : 0.004 0.049 4357 Dihedral : 5.203 166.755 3409 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.05 % Allowed : 11.45 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3114 helix: 1.91 (0.15), residues: 1251 sheet: 0.46 (0.23), residues: 540 loop : -0.18 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.016 0.001 PHE B 494 TYR 0.011 0.001 TYR E 341 ARG 0.002 0.000 ARG D 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.28 seconds wall clock time: 91 minutes 33.72 seconds (5493.72 seconds total)