Starting phenix.real_space_refine on Fri Jun 20 22:43:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygv_39271/06_2025/8ygv_39271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygv_39271/06_2025/8ygv_39271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygv_39271/06_2025/8ygv_39271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygv_39271/06_2025/8ygv_39271.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygv_39271/06_2025/8ygv_39271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygv_39271/06_2025/8ygv_39271.cif" } resolution = 3.3 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 15199 2.51 5 N 4184 2.21 5 O 4574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24034 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3649 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "B" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3649 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3649 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: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" 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: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Time building chain proxies: 14.14, per 1000 atoms: 0.59 Number of scatterers: 24034 At special positions: 0 Unit cell: (128.48, 128.48, 157.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 4574 8.00 N 4184 7.00 C 15199 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: 5.86 Conformation dependent library (CDL) restraints added in 3.1 seconds 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 26 sheets defined 47.1% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.125A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.695A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 104 " --> pdb=" O GLU A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 104' Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.618A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.859A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.881A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 removed outlier: 3.629A pdb=" N ALA A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'A' and resid 429 through 442 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 186 removed outlier: 3.979A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) 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 253 Proline residue: B 239 - end of helix removed outlier: 3.775A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.135A 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: 3.551A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 372 through 392 removed outlier: 4.471A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 405 through 420 Processing helix chain 'B' and resid 429 through 442 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 479 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.590A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.693A 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: 3.565A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.955A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 309 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 396 removed outlier: 4.541A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.797A 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 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 4.094A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.541A 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 139 through 145 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: 4.999A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.770A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.036A 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 315 through 322 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 386 Processing helix chain 'D' and resid 397 through 410 removed outlier: 3.772A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.693A pdb=" N PHE D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.744A 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 145 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 206 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: 5.471A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 removed outlier: 3.829A pdb=" N ASP E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 360 through 388 removed outlier: 4.067A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 392 Processing helix chain 'E' and resid 393 through 410 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 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.681A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 180 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 242 removed outlier: 4.975A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.752A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 308 through 312 removed outlier: 3.549A pdb=" N ASP F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 322 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 360 through 388 removed outlier: 4.111A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.675A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.585A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 41 removed outlier: 3.932A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 54 Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.818A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR G 100 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 4.760A pdb=" N PHE G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE G 126 " --> pdb=" O GLY G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 159 removed outlier: 4.322A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 283 Proline residue: G 218 - end of helix removed outlier: 3.627A pdb=" N THR G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 33 removed outlier: 6.501A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.510A pdb=" N ARG A 127 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.023A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 66 removed outlier: 3.569A pdb=" N ALA B 63 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 88 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.785A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.952A 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 Processing sheet with id=AB1, first strand: chain 'C' and resid 28 through 33 removed outlier: 6.627A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.518A 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: 4.373A 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: 3.599A pdb=" N LEU C 257 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 318 through 321 removed outlier: 8.197A pdb=" N VAL C 319 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR C 321 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 169 " --> pdb=" O THR C 321 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE C 343 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.842A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.556A pdb=" N VAL D 184 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 155 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 328 " --> pdb=" O THR D 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.513A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 10 removed outlier: 5.481A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU E 54 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AC2, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.376A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY E 298 " --> pdb=" O THR E 295 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.376A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.454A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC6, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.633A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA F 305 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR F 329 " --> pdb=" O GLY F 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 134 through 135 removed outlier: 3.813A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.077A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) 1190 hydrogen bonds defined for protein. 3417 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: 8.10 Time building geometry restraints manager: 6.89 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: 8201 1.34 - 1.46: 4845 1.46 - 1.58: 11235 1.58 - 1.70: 1 1.70 - 1.82: 154 Bond restraints: 24436 Sorted by residual: bond pdb=" CG PRO G 207 " pdb=" CD PRO G 207 " ideal model delta sigma weight residual 1.503 1.434 0.069 3.40e-02 8.65e+02 4.09e+00 bond pdb=" CB PRO G 207 " pdb=" CG PRO G 207 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.22e+00 bond pdb=" CG1 ILE F 168 " pdb=" CD1 ILE F 168 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.25e+00 bond pdb=" CG MET A 250 " pdb=" SD MET A 250 " ideal model delta sigma weight residual 1.803 1.770 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CA GLN A 113 " pdb=" CB GLN A 113 " ideal model delta sigma weight residual 1.534 1.517 0.016 1.30e-02 5.92e+03 1.56e+00 ... (remaining 24431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 32784 2.67 - 5.35: 286 5.35 - 8.02: 27 8.02 - 10.69: 4 10.69 - 13.37: 2 Bond angle restraints: 33103 Sorted by residual: angle pdb=" CA PRO G 207 " pdb=" N PRO G 207 " pdb=" CD PRO G 207 " ideal model delta sigma weight residual 112.00 102.27 9.73 1.40e+00 5.10e-01 4.83e+01 angle pdb=" C PHE G 42 " pdb=" N VAL G 43 " pdb=" CA VAL G 43 " ideal model delta sigma weight residual 120.24 123.64 -3.40 6.30e-01 2.52e+00 2.91e+01 angle pdb=" CB MET D 64 " pdb=" CG MET D 64 " pdb=" SD MET D 64 " ideal model delta sigma weight residual 112.70 126.07 -13.37 3.00e+00 1.11e-01 1.99e+01 angle pdb=" N PRO G 207 " pdb=" CD PRO G 207 " pdb=" CG PRO G 207 " ideal model delta sigma weight residual 103.20 96.54 6.66 1.50e+00 4.44e-01 1.97e+01 angle pdb=" N VAL D 162 " pdb=" CA VAL D 162 " pdb=" C VAL D 162 " ideal model delta sigma weight residual 113.53 109.36 4.17 9.80e-01 1.04e+00 1.81e+01 ... (remaining 33098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13075 17.92 - 35.84: 1407 35.84 - 53.76: 299 53.76 - 71.68: 66 71.68 - 89.60: 30 Dihedral angle restraints: 14877 sinusoidal: 5958 harmonic: 8919 Sorted by residual: dihedral pdb=" CA TYR F 341 " pdb=" C TYR F 341 " pdb=" N PRO F 342 " pdb=" CA PRO F 342 " ideal model delta harmonic sigma weight residual 180.00 144.12 35.88 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA GLN F 217 " pdb=" C GLN F 217 " pdb=" N MET F 218 " pdb=" CA MET F 218 " ideal model delta harmonic sigma weight residual 180.00 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PHE A 249 " pdb=" C PHE A 249 " pdb=" N MET A 250 " pdb=" CA MET A 250 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 14874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3327 0.069 - 0.138: 488 0.138 - 0.207: 8 0.207 - 0.276: 0 0.276 - 0.344: 2 Chirality restraints: 3825 Sorted by residual: chirality pdb=" CG LEU B 382 " pdb=" CB LEU B 382 " pdb=" CD1 LEU B 382 " pdb=" CD2 LEU B 382 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CG LEU C 384 " pdb=" CB LEU C 384 " pdb=" CD1 LEU C 384 " pdb=" CD2 LEU C 384 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE B 357 " pdb=" N ILE B 357 " pdb=" C ILE B 357 " pdb=" CB ILE B 357 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 3822 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 206 " -0.069 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO G 207 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO G 207 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO G 207 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 428 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO F 429 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 429 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 429 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 253 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" CD GLU G 253 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU G 253 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU G 253 " -0.015 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 2 2.01 - 2.73: 1864 2.73 - 3.45: 36041 3.45 - 4.18: 53466 4.18 - 4.90: 99365 Nonbonded interactions: 190738 Sorted by model distance: nonbonded pdb=" CD1 ILE B 159 " pdb=" OE1 GLU B 165 " model vdw 1.283 3.460 nonbonded pdb=" OE1 GLN B 163 " pdb=" OE2 GLU B 165 " model vdw 1.817 3.040 nonbonded pdb=" CD1 ILE B 159 " pdb=" CD GLU B 165 " model vdw 2.090 3.690 nonbonded pdb=" NH2 ARG B 412 " pdb=" O LEU B 440 " model vdw 2.164 3.120 nonbonded pdb=" NH1 ARG B 140 " pdb=" O SER B 141 " model vdw 2.186 3.120 ... (remaining 190733 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' } 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: 2.730 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: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 53.070 Find NCS groups from input model: 0.790 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.005 0.090 24436 Z= 0.205 Angle : 0.661 13.367 33103 Z= 0.360 Chirality : 0.046 0.344 3825 Planarity : 0.005 0.099 4349 Dihedral : 15.825 89.602 9169 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.35 % Allowed : 18.99 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3113 helix: 1.26 (0.15), residues: 1250 sheet: -0.43 (0.23), residues: 484 loop : -0.52 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 107 PHE 0.017 0.001 PHE B 460 TYR 0.017 0.001 TYR G 78 ARG 0.005 0.000 ARG F 405 Details of bonding type rmsd hydrogen bonds : bond 0.14246 ( 1175) hydrogen bonds : angle 6.23355 ( 3417) covalent geometry : bond 0.00464 (24436) covalent geometry : angle 0.66103 (33103) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LEU cc_start: 0.9085 (mt) cc_final: 0.8884 (mt) REVERT: D 202 MET cc_start: 0.8586 (mtm) cc_final: 0.8317 (mpp) REVERT: D 255 PHE cc_start: 0.7885 (t80) cc_final: 0.7684 (t80) REVERT: G 131 MET cc_start: 0.3853 (mmm) cc_final: 0.3168 (mmm) REVERT: G 219 GLN cc_start: 0.6615 (mm-40) cc_final: 0.6365 (tp40) outliers start: 9 outliers final: 4 residues processed: 166 average time/residue: 0.3555 time to fit residues: 95.6864 Evaluate side-chains 157 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 456 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C 467 ASN D 177 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.097458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.072069 restraints weight = 70018.770| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.93 r_work: 0.3098 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24436 Z= 0.270 Angle : 0.639 8.939 33103 Z= 0.336 Chirality : 0.047 0.240 3825 Planarity : 0.005 0.061 4349 Dihedral : 4.573 36.585 3403 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.05 % Allowed : 17.82 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3113 helix: 1.14 (0.15), residues: 1243 sheet: -0.54 (0.23), residues: 490 loop : -0.58 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 107 PHE 0.016 0.002 PHE G 165 TYR 0.018 0.002 TYR G 78 ARG 0.005 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.05146 ( 1175) hydrogen bonds : angle 5.11479 ( 3417) covalent geometry : bond 0.00629 (24436) covalent geometry : angle 0.63872 (33103) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 160 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 445 LEU cc_start: 0.9177 (mt) cc_final: 0.8935 (mt) REVERT: C 138 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8722 (t0) REVERT: D 32 ILE cc_start: 0.9257 (mt) cc_final: 0.8991 (tt) REVERT: D 64 MET cc_start: 0.8992 (mmm) cc_final: 0.8750 (mmm) REVERT: F 56 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8339 (t0) REVERT: F 74 MET cc_start: 0.8807 (mmt) cc_final: 0.8315 (mmt) REVERT: G 146 PHE cc_start: 0.7546 (t80) cc_final: 0.7236 (t80) REVERT: G 219 GLN cc_start: 0.6625 (mm-40) cc_final: 0.6390 (tp40) outliers start: 78 outliers final: 36 residues processed: 225 average time/residue: 0.3267 time to fit residues: 121.5705 Evaluate side-chains 186 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 188 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 258 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 294 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN C 466 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 GLN G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.101573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075795 restraints weight = 67992.749| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.92 r_work: 0.3151 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24436 Z= 0.118 Angle : 0.529 8.740 33103 Z= 0.276 Chirality : 0.044 0.191 3825 Planarity : 0.005 0.103 4349 Dihedral : 4.227 35.347 3401 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.86 % Allowed : 18.60 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3113 helix: 1.45 (0.15), residues: 1241 sheet: -0.34 (0.23), residues: 485 loop : -0.40 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 107 PHE 0.014 0.001 PHE G 165 TYR 0.015 0.001 TYR G 78 ARG 0.004 0.000 ARG G 34 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 1175) hydrogen bonds : angle 4.76265 ( 3417) covalent geometry : bond 0.00269 (24436) covalent geometry : angle 0.52950 (33103) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 170 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8469 (p) REVERT: A 445 LEU cc_start: 0.9127 (mt) cc_final: 0.8872 (mt) REVERT: C 138 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8709 (t0) REVERT: C 382 LEU cc_start: 0.8969 (tt) cc_final: 0.8354 (mp) REVERT: D 32 ILE cc_start: 0.9267 (mt) cc_final: 0.9026 (tt) REVERT: E 201 GLU cc_start: 0.9089 (tp30) cc_final: 0.8678 (tp30) REVERT: E 312 ASP cc_start: 0.8906 (t0) cc_final: 0.8705 (t0) REVERT: F 74 MET cc_start: 0.8775 (mmt) cc_final: 0.8269 (mmt) outliers start: 73 outliers final: 34 residues processed: 225 average time/residue: 0.2992 time to fit residues: 112.8621 Evaluate side-chains 193 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 205 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 296 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 172 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS C 322 GLN C 466 GLN D 169 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN G 209 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.093153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068896 restraints weight = 69833.116| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.98 r_work: 0.3061 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 24436 Z= 0.381 Angle : 0.738 9.310 33103 Z= 0.385 Chirality : 0.050 0.180 3825 Planarity : 0.006 0.096 4349 Dihedral : 4.829 37.169 3400 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.46 % Allowed : 18.72 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3113 helix: 0.87 (0.14), residues: 1234 sheet: -0.62 (0.23), residues: 479 loop : -0.76 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 173 PHE 0.017 0.002 PHE C 463 TYR 0.018 0.002 TYR G 78 ARG 0.008 0.001 ARG F 227 Details of bonding type rmsd hydrogen bonds : bond 0.05736 ( 1175) hydrogen bonds : angle 5.19379 ( 3417) covalent geometry : bond 0.00883 (24436) covalent geometry : angle 0.73754 (33103) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 150 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8619 (p) REVERT: A 245 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8832 (mtm) REVERT: C 138 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8629 (t0) REVERT: C 382 LEU cc_start: 0.8921 (tt) cc_final: 0.8307 (mp) REVERT: D 456 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8560 (t) REVERT: E 201 GLU cc_start: 0.9082 (tp30) cc_final: 0.8734 (tp30) REVERT: F 56 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8401 (t0) REVERT: F 74 MET cc_start: 0.8985 (mmt) cc_final: 0.8460 (mmt) REVERT: F 284 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8771 (mt-10) REVERT: G 131 MET cc_start: 0.3986 (mmm) cc_final: 0.3673 (mmt) outliers start: 114 outliers final: 72 residues processed: 251 average time/residue: 0.3027 time to fit residues: 127.3177 Evaluate side-chains 219 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 142 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 322 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 288 optimal weight: 7.9990 chunk 262 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 286 optimal weight: 0.0170 chunk 110 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 345 GLN C 397 GLN C 466 GLN D 381 GLN E 423 GLN G 209 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071946 restraints weight = 70136.493| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.75 r_work: 0.3266 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24436 Z= 0.112 Angle : 0.536 8.060 33103 Z= 0.279 Chirality : 0.044 0.219 3825 Planarity : 0.004 0.087 4349 Dihedral : 4.295 36.052 3400 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.52 % Allowed : 19.73 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3113 helix: 1.40 (0.15), residues: 1228 sheet: -0.36 (0.23), residues: 480 loop : -0.51 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 107 PHE 0.015 0.001 PHE B 460 TYR 0.013 0.001 TYR G 78 ARG 0.007 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 1175) hydrogen bonds : angle 4.74239 ( 3417) covalent geometry : bond 0.00250 (24436) covalent geometry : angle 0.53599 (33103) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 163 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 245 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8737 (mtm) REVERT: A 445 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8896 (mt) REVERT: B 404 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7859 (ptpp) REVERT: C 48 MET cc_start: 0.8767 (mtm) cc_final: 0.8533 (mtt) REVERT: C 51 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: C 138 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8652 (t0) REVERT: C 382 LEU cc_start: 0.8901 (tt) cc_final: 0.8265 (mp) REVERT: D 32 ILE cc_start: 0.9273 (mt) cc_final: 0.9054 (tt) REVERT: D 456 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8056 (p) REVERT: E 64 MET cc_start: 0.9270 (mmt) cc_final: 0.8838 (mmt) REVERT: E 201 GLU cc_start: 0.8902 (tp30) cc_final: 0.8549 (tp30) REVERT: F 64 MET cc_start: 0.9026 (mmm) cc_final: 0.8688 (mmp) REVERT: F 74 MET cc_start: 0.8791 (mmt) cc_final: 0.8230 (mmt) REVERT: F 469 MET cc_start: 0.6848 (ptt) cc_final: 0.6260 (ptm) REVERT: G 209 GLN cc_start: 0.7297 (tp-100) cc_final: 0.7021 (pm20) outliers start: 90 outliers final: 45 residues processed: 237 average time/residue: 0.4765 time to fit residues: 184.1409 Evaluate side-chains 205 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 205 PHE Chi-restraints excluded: chain G residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 118 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 chunk 124 optimal weight: 9.9990 chunk 87 optimal weight: 0.3980 chunk 299 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 GLN G 174 HIS G 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.100453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072626 restraints weight = 69746.523| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.78 r_work: 0.3218 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24436 Z= 0.108 Angle : 0.528 12.336 33103 Z= 0.271 Chirality : 0.044 0.318 3825 Planarity : 0.004 0.084 4349 Dihedral : 4.086 35.094 3400 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.98 % Allowed : 20.01 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3113 helix: 1.59 (0.15), residues: 1222 sheet: -0.25 (0.23), residues: 485 loop : -0.40 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 107 PHE 0.013 0.001 PHE C 463 TYR 0.013 0.001 TYR G 78 ARG 0.007 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 1175) hydrogen bonds : angle 4.63798 ( 3417) covalent geometry : bond 0.00246 (24436) covalent geometry : angle 0.52774 (33103) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 159 time to evaluate : 2.964 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 245 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8887 (mtm) REVERT: A 350 PHE cc_start: 0.8801 (t80) cc_final: 0.8548 (m-10) REVERT: A 445 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8978 (mt) REVERT: B 404 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7623 (pttp) REVERT: C 51 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: C 341 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: D 32 ILE cc_start: 0.9273 (mt) cc_final: 0.9031 (tt) REVERT: D 456 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8011 (p) REVERT: E 64 MET cc_start: 0.9289 (mmt) cc_final: 0.8823 (mmt) REVERT: E 201 GLU cc_start: 0.8979 (tp30) cc_final: 0.8591 (tp30) REVERT: E 333 ARG cc_start: 0.8667 (tpp80) cc_final: 0.8294 (tpp80) REVERT: F 74 MET cc_start: 0.8776 (mmt) cc_final: 0.8172 (mmt) REVERT: F 461 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: F 469 MET cc_start: 0.6908 (ptt) cc_final: 0.6343 (ptm) REVERT: G 131 MET cc_start: 0.3937 (mmm) cc_final: 0.3467 (mmm) REVERT: G 205 PHE cc_start: 0.3103 (OUTLIER) cc_final: 0.1757 (m-10) REVERT: G 209 GLN cc_start: 0.7303 (tp40) cc_final: 0.6693 (pm20) outliers start: 76 outliers final: 42 residues processed: 222 average time/residue: 0.3163 time to fit residues: 118.7095 Evaluate side-chains 205 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 461 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 205 PHE Chi-restraints excluded: chain G residue 229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 194 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 295 optimal weight: 20.0000 chunk 136 optimal weight: 0.0030 chunk 64 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN G 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.096864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072242 restraints weight = 69410.744| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.78 r_work: 0.3138 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 24436 Z= 0.256 Angle : 0.639 12.981 33103 Z= 0.328 Chirality : 0.047 0.275 3825 Planarity : 0.005 0.087 4349 Dihedral : 4.395 36.011 3400 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.37 % Allowed : 20.48 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3113 helix: 1.31 (0.15), residues: 1225 sheet: -0.42 (0.23), residues: 480 loop : -0.55 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 173 PHE 0.016 0.002 PHE C 494 TYR 0.017 0.001 TYR G 78 ARG 0.008 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 1175) hydrogen bonds : angle 4.90909 ( 3417) covalent geometry : bond 0.00599 (24436) covalent geometry : angle 0.63943 (33103) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 156 time to evaluate : 2.759 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8839 (mtm) REVERT: A 350 PHE cc_start: 0.8785 (t80) cc_final: 0.8575 (m-10) REVERT: B 345 GLN cc_start: 0.8626 (mt0) cc_final: 0.8064 (mt0) REVERT: B 404 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7681 (pttp) REVERT: C 51 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: C 382 LEU cc_start: 0.8960 (tt) cc_final: 0.8323 (mp) REVERT: D 32 ILE cc_start: 0.9325 (mt) cc_final: 0.9015 (tt) REVERT: D 456 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8460 (t) REVERT: E 201 GLU cc_start: 0.9065 (tp30) cc_final: 0.8581 (tp30) REVERT: E 333 ARG cc_start: 0.8778 (tpp80) cc_final: 0.8414 (tpp80) REVERT: F 469 MET cc_start: 0.6999 (ptt) cc_final: 0.6479 (ptm) REVERT: G 131 MET cc_start: 0.3417 (mmm) cc_final: 0.3061 (mmm) outliers start: 86 outliers final: 61 residues processed: 227 average time/residue: 0.3076 time to fit residues: 117.9778 Evaluate side-chains 216 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 205 PHE Chi-restraints excluded: chain G residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 283 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.100266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075617 restraints weight = 68645.193| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.80 r_work: 0.3239 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24436 Z= 0.153 Angle : 0.575 12.784 33103 Z= 0.292 Chirality : 0.045 0.267 3825 Planarity : 0.004 0.083 4349 Dihedral : 4.240 35.956 3400 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.21 % Allowed : 20.83 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3113 helix: 1.46 (0.15), residues: 1222 sheet: -0.31 (0.23), residues: 480 loop : -0.50 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 173 PHE 0.015 0.001 PHE G 165 TYR 0.014 0.001 TYR G 78 ARG 0.006 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 1175) hydrogen bonds : angle 4.75810 ( 3417) covalent geometry : bond 0.00359 (24436) covalent geometry : angle 0.57467 (33103) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 158 time to evaluate : 2.562 Fit side-chains REVERT: A 245 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8795 (mtm) REVERT: B 345 GLN cc_start: 0.8663 (mt0) cc_final: 0.8160 (mt0) REVERT: B 404 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7666 (pttp) REVERT: C 51 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: C 382 LEU cc_start: 0.8959 (tt) cc_final: 0.8339 (mp) REVERT: D 32 ILE cc_start: 0.9297 (mt) cc_final: 0.9039 (tt) REVERT: D 456 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8399 (t) REVERT: E 64 MET cc_start: 0.9308 (mmt) cc_final: 0.8835 (mmt) REVERT: E 201 GLU cc_start: 0.8990 (tp30) cc_final: 0.8613 (tp30) REVERT: E 311 ASP cc_start: 0.9195 (t70) cc_final: 0.8894 (t70) REVERT: E 333 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8460 (tpp80) REVERT: F 74 MET cc_start: 0.8792 (mmt) cc_final: 0.8077 (mmt) REVERT: F 469 MET cc_start: 0.7127 (ptt) cc_final: 0.6605 (ptm) REVERT: G 131 MET cc_start: 0.3844 (mmm) cc_final: 0.3536 (mmm) REVERT: G 205 PHE cc_start: 0.3381 (OUTLIER) cc_final: 0.2304 (m-10) REVERT: G 209 GLN cc_start: 0.7406 (tp-100) cc_final: 0.6951 (tp40) outliers start: 82 outliers final: 60 residues processed: 229 average time/residue: 0.3054 time to fit residues: 116.0069 Evaluate side-chains 217 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 431 LYS Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 205 PHE Chi-restraints excluded: chain G residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 309 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN G 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.100292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.075387 restraints weight = 68412.148| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.86 r_work: 0.3178 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24436 Z= 0.111 Angle : 0.551 12.770 33103 Z= 0.278 Chirality : 0.044 0.289 3825 Planarity : 0.004 0.080 4349 Dihedral : 4.031 34.984 3400 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.55 % Allowed : 21.53 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3113 helix: 1.62 (0.15), residues: 1222 sheet: -0.14 (0.24), residues: 461 loop : -0.41 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 65 PHE 0.013 0.001 PHE G 165 TYR 0.012 0.001 TYR G 78 ARG 0.005 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1175) hydrogen bonds : angle 4.63561 ( 3417) covalent geometry : bond 0.00253 (24436) covalent geometry : angle 0.55095 (33103) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 2.530 Fit side-chains REVERT: A 373 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8200 (ptmm) REVERT: B 345 GLN cc_start: 0.8604 (mt0) cc_final: 0.8130 (mt0) REVERT: B 404 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7709 (pttp) REVERT: C 51 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: D 32 ILE cc_start: 0.9282 (mt) cc_final: 0.9008 (tt) REVERT: D 456 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8013 (p) REVERT: E 64 MET cc_start: 0.9285 (mmt) cc_final: 0.8811 (mmt) REVERT: E 201 GLU cc_start: 0.8984 (tp30) cc_final: 0.8567 (tp30) REVERT: E 333 ARG cc_start: 0.8795 (tpp80) cc_final: 0.8454 (tpp80) REVERT: F 74 MET cc_start: 0.8843 (mmt) cc_final: 0.8134 (mmt) REVERT: F 171 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8819 (mp) REVERT: F 469 MET cc_start: 0.7099 (ptt) cc_final: 0.6602 (ptm) REVERT: G 131 MET cc_start: 0.3786 (mmm) cc_final: 0.3528 (mmm) outliers start: 65 outliers final: 52 residues processed: 221 average time/residue: 0.3015 time to fit residues: 110.4305 Evaluate side-chains 208 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 227 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 268 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.099124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074411 restraints weight = 69320.130| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.21 r_work: 0.3236 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24436 Z= 0.155 Angle : 0.588 12.976 33103 Z= 0.296 Chirality : 0.045 0.263 3825 Planarity : 0.004 0.082 4349 Dihedral : 4.088 35.222 3400 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.47 % Allowed : 21.81 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3113 helix: 1.52 (0.15), residues: 1231 sheet: -0.19 (0.24), residues: 473 loop : -0.41 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 65 PHE 0.017 0.001 PHE G 165 TYR 0.015 0.001 TYR G 78 ARG 0.005 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 1175) hydrogen bonds : angle 4.69017 ( 3417) covalent geometry : bond 0.00366 (24436) covalent geometry : angle 0.58755 (33103) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 2.703 Fit side-chains REVERT: B 345 GLN cc_start: 0.8611 (mt0) cc_final: 0.8140 (mt0) REVERT: B 404 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7700 (pttp) REVERT: C 51 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: D 32 ILE cc_start: 0.9314 (mt) cc_final: 0.9042 (tt) REVERT: D 456 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8320 (t) REVERT: E 64 MET cc_start: 0.9305 (mmt) cc_final: 0.8849 (mmt) REVERT: E 201 GLU cc_start: 0.8949 (tp30) cc_final: 0.8552 (tp30) REVERT: E 333 ARG cc_start: 0.8795 (tpp80) cc_final: 0.8516 (tpp80) REVERT: F 74 MET cc_start: 0.8821 (mmt) cc_final: 0.8114 (mmt) REVERT: F 171 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8870 (mp) REVERT: F 469 MET cc_start: 0.7067 (ptt) cc_final: 0.6614 (ptm) REVERT: G 131 MET cc_start: 0.3729 (mmm) cc_final: 0.3456 (mmm) outliers start: 63 outliers final: 54 residues processed: 214 average time/residue: 0.3082 time to fit residues: 110.0384 Evaluate side-chains 210 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 152 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 194 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 271 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN C 466 GLN D 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.097402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071202 restraints weight = 70363.665| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.00 r_work: 0.3090 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24436 Z= 0.260 Angle : 0.679 13.988 33103 Z= 0.345 Chirality : 0.047 0.267 3825 Planarity : 0.005 0.086 4349 Dihedral : 4.428 35.999 3400 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.98 % Allowed : 21.50 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3113 helix: 1.27 (0.15), residues: 1225 sheet: -0.39 (0.23), residues: 477 loop : -0.55 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 173 PHE 0.019 0.002 PHE B 460 TYR 0.018 0.001 TYR G 78 ARG 0.006 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 1175) hydrogen bonds : angle 4.90945 ( 3417) covalent geometry : bond 0.00609 (24436) covalent geometry : angle 0.67898 (33103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12871.72 seconds wall clock time: 223 minutes 23.36 seconds (13403.36 seconds total)