Starting phenix.real_space_refine on Fri Sep 19 07:31:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygv_39271/09_2025/8ygv_39271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygv_39271/09_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_39271/09_2025/8ygv_39271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygv_39271/09_2025/8ygv_39271.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygv_39271/09_2025/8ygv_39271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygv_39271/09_2025/8ygv_39271.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.26, per 1000 atoms: 0.22 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: 1.74 Conformation dependent library (CDL) restraints added in 990.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.81 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: 4.49 Time building geometry restraints manager: 2.22 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: 4.170 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.760 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG F 405 TYR 0.017 0.001 TYR G 78 PHE 0.017 0.001 PHE B 460 HIS 0.005 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00464 (24436) covalent geometry : angle 0.66103 (33103) hydrogen bonds : bond 0.14246 ( 1175) hydrogen bonds : angle 6.23355 ( 3417) *********************** 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 : 0.921 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: 0.1519 time to fit residues: 40.3484 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 : 0.714 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 2.7764 ------------------------------------------------------------------------------- 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** G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.098984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073484 restraints weight = 69480.156| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.94 r_work: 0.3113 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24436 Z= 0.185 Angle : 0.574 8.345 33103 Z= 0.302 Chirality : 0.045 0.228 3825 Planarity : 0.005 0.061 4349 Dihedral : 4.377 36.199 3403 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.43 % Allowed : 17.62 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 3113 helix: 1.35 (0.15), residues: 1242 sheet: -0.40 (0.23), residues: 497 loop : -0.41 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.016 0.001 TYR G 78 PHE 0.018 0.001 PHE G 165 HIS 0.006 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00430 (24436) covalent geometry : angle 0.57354 (33103) hydrogen bonds : bond 0.04542 ( 1175) hydrogen bonds : angle 4.97729 ( 3417) *********************** 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 228 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8561 (p) REVERT: A 445 LEU cc_start: 0.9155 (mt) cc_final: 0.8916 (mt) REVERT: C 138 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8746 (t0) REVERT: D 32 ILE cc_start: 0.9244 (mt) cc_final: 0.9004 (tt) REVERT: F 74 MET cc_start: 0.8676 (mmt) cc_final: 0.8206 (mmt) REVERT: G 46 MET cc_start: 0.8047 (tpp) cc_final: 0.7776 (tmm) REVERT: G 146 PHE cc_start: 0.7512 (t80) cc_final: 0.7210 (t80) REVERT: G 219 GLN cc_start: 0.6593 (mm-40) cc_final: 0.6363 (tp40) outliers start: 62 outliers final: 24 residues processed: 216 average time/residue: 0.1341 time to fit residues: 47.3465 Evaluate side-chains 176 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 108 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain D residue 162 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 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 57 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 301 THR 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 188 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 7 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.105479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081658 restraints weight = 71041.291| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.83 r_work: 0.3193 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24436 Z= 0.113 Angle : 0.516 8.670 33103 Z= 0.269 Chirality : 0.044 0.201 3825 Planarity : 0.004 0.097 4349 Dihedral : 4.103 34.963 3400 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.90 % Allowed : 18.25 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.15), residues: 3113 helix: 1.57 (0.15), residues: 1238 sheet: -0.25 (0.23), residues: 495 loop : -0.34 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 227 TYR 0.015 0.001 TYR G 78 PHE 0.018 0.001 PHE D 255 HIS 0.005 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00256 (24436) covalent geometry : angle 0.51649 (33103) hydrogen bonds : bond 0.03901 ( 1175) hydrogen bonds : angle 4.68969 ( 3417) *********************** 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 245 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 171 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8493 (p) REVERT: A 445 LEU cc_start: 0.9161 (mt) cc_final: 0.8910 (mt) REVERT: C 382 LEU cc_start: 0.8979 (tt) cc_final: 0.8369 (mp) REVERT: C 392 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7245 (tp) REVERT: D 32 ILE cc_start: 0.9288 (mt) cc_final: 0.9067 (tt) REVERT: D 201 GLU cc_start: 0.9255 (tt0) cc_final: 0.9055 (tt0) REVERT: E 201 GLU cc_start: 0.9067 (tp30) cc_final: 0.8670 (tp30) REVERT: F 64 MET cc_start: 0.9087 (mmm) cc_final: 0.8877 (mmp) REVERT: F 74 MET cc_start: 0.8657 (mmt) cc_final: 0.8071 (mmt) REVERT: G 146 PHE cc_start: 0.7412 (t80) cc_final: 0.7144 (t80) outliers start: 74 outliers final: 33 residues processed: 227 average time/residue: 0.1281 time to fit residues: 49.0025 Evaluate side-chains 187 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 314 THR Chi-restraints excluded: chain B residue 366 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 95 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 254 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 141 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 284 GLU 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 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 117 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 305 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 295 optimal weight: 0.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN C 466 GLN E 304 GLN F 365 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.100444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075014 restraints weight = 68968.458| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.29 r_work: 0.3197 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24436 Z= 0.129 Angle : 0.519 9.181 33103 Z= 0.269 Chirality : 0.044 0.235 3825 Planarity : 0.004 0.087 4349 Dihedral : 4.042 35.138 3400 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.17 % Allowed : 18.36 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.15), residues: 3113 helix: 1.61 (0.15), residues: 1244 sheet: -0.19 (0.23), residues: 500 loop : -0.34 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 412 TYR 0.015 0.001 TYR G 78 PHE 0.014 0.001 PHE G 165 HIS 0.005 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00298 (24436) covalent geometry : angle 0.51889 (33103) hydrogen bonds : bond 0.03858 ( 1175) hydrogen bonds : angle 4.61567 ( 3417) *********************** 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 238 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 157 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8462 (p) REVERT: A 350 PHE cc_start: 0.8823 (t80) cc_final: 0.8485 (m-10) REVERT: A 445 LEU cc_start: 0.9153 (mt) cc_final: 0.8894 (mt) REVERT: C 392 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7218 (tp) REVERT: D 32 ILE cc_start: 0.9298 (mt) cc_final: 0.9061 (tt) REVERT: D 201 GLU cc_start: 0.9275 (tt0) cc_final: 0.9070 (tt0) REVERT: E 201 GLU cc_start: 0.9024 (tp30) cc_final: 0.8573 (tp30) REVERT: E 312 ASP cc_start: 0.8829 (t0) cc_final: 0.8604 (t0) REVERT: F 74 MET cc_start: 0.8723 (mmt) cc_final: 0.8178 (mmt) REVERT: G 46 MET cc_start: 0.7822 (tmm) cc_final: 0.7444 (tpt) outliers start: 81 outliers final: 49 residues processed: 223 average time/residue: 0.1239 time to fit residues: 46.4057 Evaluate side-chains 202 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 157 VAL 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 381 THR 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 314 THR Chi-restraints excluded: chain B residue 366 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 159 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 392 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 262 SER Chi-restraints excluded: chain D residue 275 VAL 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 301 THR 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 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 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 6 ASP 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 259 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 264 optimal weight: 0.6980 chunk 222 optimal weight: 8.9990 chunk 198 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 286 optimal weight: 0.0470 chunk 102 optimal weight: 6.9990 overall best weight: 2.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN C 466 GLN D 169 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.099761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.074195 restraints weight = 69213.922| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 4.27 r_work: 0.3131 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24436 Z= 0.158 Angle : 0.538 9.241 33103 Z= 0.278 Chirality : 0.044 0.273 3825 Planarity : 0.004 0.079 4349 Dihedral : 4.085 35.429 3400 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.56 % Allowed : 18.99 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3113 helix: 1.61 (0.15), residues: 1231 sheet: -0.27 (0.23), residues: 481 loop : -0.31 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 154 TYR 0.015 0.001 TYR G 78 PHE 0.015 0.001 PHE G 165 HIS 0.005 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00369 (24436) covalent geometry : angle 0.53758 (33103) hydrogen bonds : bond 0.04019 ( 1175) hydrogen bonds : angle 4.65139 ( 3417) *********************** 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 248 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 157 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 350 PHE cc_start: 0.8886 (t80) cc_final: 0.8529 (m-10) REVERT: A 445 LEU cc_start: 0.9175 (mt) cc_final: 0.8921 (mt) REVERT: C 392 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7266 (tt) REVERT: D 32 ILE cc_start: 0.9296 (mt) cc_final: 0.9020 (tt) REVERT: D 201 GLU cc_start: 0.9356 (tt0) cc_final: 0.9155 (tt0) REVERT: E 201 GLU cc_start: 0.9086 (tp30) cc_final: 0.8610 (tp30) REVERT: E 311 ASP cc_start: 0.9224 (t70) cc_final: 0.8948 (t70) REVERT: E 312 ASP cc_start: 0.8904 (t0) cc_final: 0.8659 (t0) REVERT: F 74 MET cc_start: 0.8846 (mmt) cc_final: 0.8245 (mmt) REVERT: F 469 MET cc_start: 0.7017 (ptt) cc_final: 0.6405 (ptm) REVERT: G 46 MET cc_start: 0.7843 (tmm) cc_final: 0.7471 (tpt) outliers start: 91 outliers final: 58 residues processed: 235 average time/residue: 0.1277 time to fit residues: 50.0250 Evaluate side-chains 214 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 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 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 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 66 LEU 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 386 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 410 LEU 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 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 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 283 THR Chi-restraints excluded: chain E residue 284 GLU 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 7 ILE 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 6 ASP 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 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 58 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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** C 322 GLN C 345 GLN C 466 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 = 0.3753 r_free = 0.3753 target = 0.097101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071720 restraints weight = 70035.708| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 4.25 r_work: 0.3175 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24436 Z= 0.257 Angle : 0.627 9.480 33103 Z= 0.324 Chirality : 0.046 0.193 3825 Planarity : 0.005 0.081 4349 Dihedral : 4.404 36.253 3400 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.80 % Allowed : 19.34 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.15), residues: 3113 helix: 1.32 (0.15), residues: 1231 sheet: -0.43 (0.23), residues: 475 loop : -0.50 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 240 TYR 0.016 0.001 TYR G 78 PHE 0.017 0.002 PHE G 165 HIS 0.007 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00599 (24436) covalent geometry : angle 0.62723 (33103) hydrogen bonds : bond 0.04829 ( 1175) hydrogen bonds : angle 4.86187 ( 3417) *********************** 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 254 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 157 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8528 (p) REVERT: A 245 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8782 (mtm) REVERT: A 445 LEU cc_start: 0.9148 (mt) cc_final: 0.8901 (mt) REVERT: C 51 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: C 392 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7381 (tt) REVERT: D 32 ILE cc_start: 0.9328 (mt) cc_final: 0.9057 (tt) REVERT: D 456 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8427 (t) REVERT: E 201 GLU cc_start: 0.9015 (tp30) cc_final: 0.8591 (tp30) REVERT: E 312 ASP cc_start: 0.8843 (t0) cc_final: 0.8635 (t0) REVERT: F 74 MET cc_start: 0.8905 (mmt) cc_final: 0.8403 (mmt) REVERT: F 469 MET cc_start: 0.7007 (ptt) cc_final: 0.6459 (ptm) REVERT: G 46 MET cc_start: 0.7949 (tmm) cc_final: 0.7564 (tpt) REVERT: G 165 PHE cc_start: 0.3308 (OUTLIER) cc_final: 0.3105 (t80) outliers start: 97 outliers final: 70 residues processed: 241 average time/residue: 0.1243 time to fit residues: 50.9530 Evaluate side-chains 223 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 147 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 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 297 LEU Chi-restraints excluded: chain B residue 314 THR 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 36 ASP 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 144 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 257 LEU 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 C residue 392 LEU Chi-restraints excluded: chain C residue 410 LEU 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 228 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 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 233 LEU 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 61 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 228 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 456 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 52 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 165 PHE Chi-restraints excluded: chain G residue 188 LEU 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 231 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 217 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 G 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.101805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076752 restraints weight = 69271.522| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.24 r_work: 0.3260 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24436 Z= 0.104 Angle : 0.525 8.269 33103 Z= 0.271 Chirality : 0.044 0.259 3825 Planarity : 0.004 0.074 4349 Dihedral : 4.064 35.460 3400 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.90 % Allowed : 20.63 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3113 helix: 1.64 (0.15), residues: 1225 sheet: -0.21 (0.23), residues: 489 loop : -0.31 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 333 TYR 0.012 0.001 TYR G 78 PHE 0.013 0.001 PHE B 460 HIS 0.004 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00234 (24436) covalent geometry : angle 0.52498 (33103) hydrogen bonds : bond 0.03683 ( 1175) hydrogen bonds : angle 4.59827 ( 3417) *********************** 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 233 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 159 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8388 (p) REVERT: A 245 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8859 (mtm) REVERT: A 350 PHE cc_start: 0.8799 (t80) cc_final: 0.8555 (m-10) REVERT: A 445 LEU cc_start: 0.9106 (mt) cc_final: 0.8889 (mt) REVERT: C 51 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: C 392 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7478 (tp) REVERT: D 32 ILE cc_start: 0.9278 (mt) cc_final: 0.9051 (tt) REVERT: D 456 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.7904 (p) REVERT: E 201 GLU cc_start: 0.9037 (tp30) cc_final: 0.8533 (tp30) REVERT: E 311 ASP cc_start: 0.9207 (t70) cc_final: 0.8940 (t70) REVERT: E 312 ASP cc_start: 0.8825 (t0) cc_final: 0.8559 (t0) REVERT: F 74 MET cc_start: 0.8784 (mmt) cc_final: 0.8168 (mmt) REVERT: F 469 MET cc_start: 0.6966 (ptt) cc_final: 0.6422 (ptm) REVERT: G 46 MET cc_start: 0.7965 (tmm) cc_final: 0.7624 (tpt) REVERT: G 165 PHE cc_start: 0.3325 (OUTLIER) cc_final: 0.3123 (t80) outliers start: 74 outliers final: 45 residues processed: 220 average time/residue: 0.1396 time to fit residues: 50.8142 Evaluate side-chains 204 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 320 GLU Chi-restraints excluded: chain A residue 366 VAL 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 499 VAL Chi-restraints excluded: chain C residue 25 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 341 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 410 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 275 VAL 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 141 VAL Chi-restraints excluded: chain E residue 150 LYS 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 337 GLU Chi-restraints excluded: chain E residue 456 VAL 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 52 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 165 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 149 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN C 466 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.096923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.071688 restraints weight = 69944.347| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.24 r_work: 0.3096 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1622 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= 0.274 Angle : 0.645 8.790 33103 Z= 0.333 Chirality : 0.047 0.229 3825 Planarity : 0.005 0.080 4349 Dihedral : 4.383 36.278 3400 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.41 % Allowed : 20.40 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 3113 helix: 1.32 (0.15), residues: 1231 sheet: -0.49 (0.23), residues: 480 loop : -0.50 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 139 TYR 0.016 0.001 TYR G 78 PHE 0.016 0.002 PHE C 494 HIS 0.006 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00641 (24436) covalent geometry : angle 0.64524 (33103) hydrogen bonds : bond 0.04769 ( 1175) hydrogen bonds : angle 4.85915 ( 3417) *********************** 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 241 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 154 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8911 (mtm) REVERT: A 350 PHE cc_start: 0.8878 (t80) cc_final: 0.8579 (m-10) REVERT: A 445 LEU cc_start: 0.9176 (mt) cc_final: 0.8910 (mt) REVERT: C 51 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: C 392 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7303 (tt) REVERT: D 32 ILE cc_start: 0.9318 (mt) cc_final: 0.9033 (tt) REVERT: D 456 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8423 (t) REVERT: E 201 GLU cc_start: 0.9160 (tp30) cc_final: 0.8700 (tp30) REVERT: E 312 ASP cc_start: 0.8962 (t0) cc_final: 0.8690 (t0) REVERT: F 74 MET cc_start: 0.8988 (mmt) cc_final: 0.8459 (mmt) REVERT: F 469 MET cc_start: 0.6970 (ptt) cc_final: 0.6520 (ptm) REVERT: G 165 PHE cc_start: 0.3536 (OUTLIER) cc_final: 0.3309 (t80) outliers start: 87 outliers final: 62 residues processed: 229 average time/residue: 0.1325 time to fit residues: 50.6708 Evaluate side-chains 213 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 146 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 153 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 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 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 42 HIS 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 144 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 410 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 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 182 ILE 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 337 GLU Chi-restraints excluded: chain E residue 399 VAL 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 171 LEU Chi-restraints excluded: chain F residue 228 VAL 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 456 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 52 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 165 PHE Chi-restraints excluded: chain G residue 188 LEU 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 160 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 245 optimal weight: 0.0170 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.099656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.073902 restraints weight = 69203.131| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.96 r_work: 0.3148 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24436 Z= 0.124 Angle : 0.559 10.730 33103 Z= 0.284 Chirality : 0.044 0.323 3825 Planarity : 0.004 0.074 4349 Dihedral : 4.153 35.822 3400 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.78 % Allowed : 21.18 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.15), residues: 3113 helix: 1.56 (0.15), residues: 1225 sheet: -0.23 (0.23), residues: 492 loop : -0.42 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 333 TYR 0.014 0.001 TYR G 78 PHE 0.013 0.001 PHE C 494 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00287 (24436) covalent geometry : angle 0.55924 (33103) hydrogen bonds : bond 0.03934 ( 1175) hydrogen bonds : angle 4.66616 ( 3417) *********************** 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 225 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 154 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8886 (mtm) REVERT: A 350 PHE cc_start: 0.8849 (t80) cc_final: 0.8570 (m-10) REVERT: A 445 LEU cc_start: 0.9122 (mt) cc_final: 0.8901 (mt) REVERT: B 404 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7531 (pttp) REVERT: C 51 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: C 392 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7309 (tt) REVERT: D 32 ILE cc_start: 0.9275 (mt) cc_final: 0.9032 (tt) REVERT: D 456 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8328 (t) REVERT: E 201 GLU cc_start: 0.9065 (tp30) cc_final: 0.8537 (tp30) REVERT: E 311 ASP cc_start: 0.9217 (t70) cc_final: 0.8996 (t70) REVERT: E 312 ASP cc_start: 0.8902 (t0) cc_final: 0.8612 (t0) REVERT: F 64 MET cc_start: 0.8853 (mmm) cc_final: 0.8589 (mmp) REVERT: F 74 MET cc_start: 0.8887 (mmt) cc_final: 0.8295 (mmt) REVERT: F 469 MET cc_start: 0.6893 (ptt) cc_final: 0.6442 (ptm) REVERT: G 46 MET cc_start: 0.7676 (tmm) cc_final: 0.7230 (tpt) REVERT: G 165 PHE cc_start: 0.3350 (OUTLIER) cc_final: 0.3114 (t80) outliers start: 71 outliers final: 58 residues processed: 213 average time/residue: 0.1236 time to fit residues: 44.1219 Evaluate side-chains 212 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 153 ILE 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 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 314 THR 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 C residue 392 LEU Chi-restraints excluded: chain C residue 410 LEU 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 201 GLU 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 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 150 LYS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 233 LEU 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 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 52 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 165 PHE 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 200 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 152 optimal weight: 0.3980 chunk 268 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.077107 restraints weight = 69100.834| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.26 r_work: 0.3282 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24436 Z= 0.102 Angle : 0.554 10.972 33103 Z= 0.279 Chirality : 0.044 0.287 3825 Planarity : 0.004 0.073 4349 Dihedral : 3.962 34.760 3400 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.39 % Allowed : 21.61 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.16), residues: 3113 helix: 1.74 (0.15), residues: 1219 sheet: -0.01 (0.24), residues: 482 loop : -0.28 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 333 TYR 0.026 0.001 TYR G 78 PHE 0.012 0.001 PHE C 494 HIS 0.003 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00229 (24436) covalent geometry : angle 0.55379 (33103) hydrogen bonds : bond 0.03466 ( 1175) hydrogen bonds : angle 4.57317 ( 3417) ********************** 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 224 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 PHE cc_start: 0.8800 (t80) cc_final: 0.8578 (m-10) REVERT: A 373 LYS cc_start: 0.8504 (mtmm) cc_final: 0.7915 (pttt) REVERT: A 445 LEU cc_start: 0.9047 (mt) cc_final: 0.8818 (mt) REVERT: B 404 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7534 (pttp) REVERT: B 418 GLU cc_start: 0.8878 (tp30) cc_final: 0.7960 (tm-30) REVERT: C 51 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: C 392 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7329 (tt) REVERT: C 466 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: D 32 ILE cc_start: 0.9294 (mt) cc_final: 0.9039 (tt) REVERT: D 456 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.7841 (p) REVERT: E 201 GLU cc_start: 0.9004 (tp30) cc_final: 0.8589 (tp30) REVERT: E 311 ASP cc_start: 0.9218 (t70) cc_final: 0.8983 (t70) REVERT: E 312 ASP cc_start: 0.8868 (t0) cc_final: 0.8630 (t0) REVERT: F 74 MET cc_start: 0.8756 (mmt) cc_final: 0.8183 (mmt) REVERT: F 469 MET cc_start: 0.6885 (ptt) cc_final: 0.6462 (ptm) REVERT: G 46 MET cc_start: 0.7752 (tmm) cc_final: 0.7335 (tpt) REVERT: G 165 PHE cc_start: 0.3612 (OUTLIER) cc_final: 0.3385 (t80) outliers start: 61 outliers final: 46 residues processed: 216 average time/residue: 0.1327 time to fit residues: 47.5815 Evaluate side-chains 210 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE 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 366 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 314 THR 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 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 C residue 392 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 466 GLN 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 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 233 LEU 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 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 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 80 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 165 PHE 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 204 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 267 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 174 optimal weight: 0.3980 chunk 182 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 120 optimal weight: 0.0970 chunk 240 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 287 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.099827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073226 restraints weight = 69551.567| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.04 r_work: 0.3158 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24436 Z= 0.151 Angle : 0.581 11.132 33103 Z= 0.293 Chirality : 0.045 0.307 3825 Planarity : 0.004 0.075 4349 Dihedral : 4.031 34.867 3400 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.51 % Allowed : 21.65 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.15), residues: 3113 helix: 1.65 (0.15), residues: 1231 sheet: -0.09 (0.23), residues: 487 loop : -0.34 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 333 TYR 0.019 0.001 TYR G 78 PHE 0.024 0.001 PHE B 460 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00353 (24436) covalent geometry : angle 0.58114 (33103) hydrogen bonds : bond 0.03837 ( 1175) hydrogen bonds : angle 4.61172 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5561.97 seconds wall clock time: 95 minutes 44.03 seconds (5744.03 seconds total)