Starting phenix.real_space_refine on Sat Jan 20 06:15:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssv_25414/01_2024/7ssv_25414.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssv_25414/01_2024/7ssv_25414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssv_25414/01_2024/7ssv_25414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssv_25414/01_2024/7ssv_25414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssv_25414/01_2024/7ssv_25414.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssv_25414/01_2024/7ssv_25414.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 51 5.16 5 C 8938 2.51 5 N 2365 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ARG 209": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D GLU 490": "OE1" <-> "OE2" Residue "H ARG 108": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13815 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2844 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "B" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2844 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "C" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2844 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "D" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2844 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "H" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1389 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 246} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 639 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 552 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 304 Chain: "L" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1047 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 461 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 260 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.30, per 1000 atoms: 0.53 Number of scatterers: 13815 At special positions: 0 Unit cell: (188.292, 121.836, 138.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 51 16.00 O 2458 8.00 N 2365 7.00 C 8938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 142 " distance=2.02 Simple disulfide: pdb=" SG CYS H 119 " - pdb=" SG CYS H 135 " distance=2.01 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 139 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 2.7 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3506 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 18 sheets defined 55.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.855A pdb=" N ILE A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 293 through 317 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.947A pdb=" N SER A 324 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 348 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 370 through 380 removed outlier: 3.584A pdb=" N ILE A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.533A pdb=" N LEU A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 420 removed outlier: 4.403A pdb=" N LEU A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.769A pdb=" N LYS A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.871A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.605A pdb=" N LEU B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 removed outlier: 3.917A pdb=" N SER B 155 " --> pdb=" O ASN B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 156 through 166 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.547A pdb=" N TRP B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.763A pdb=" N SER B 229 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 231 through 256 removed outlier: 3.524A pdb=" N VAL B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 316 Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.596A pdb=" N ARG B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.705A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 361 through 370 removed outlier: 4.069A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 395 through 420 removed outlier: 4.403A pdb=" N LEU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 433 Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.769A pdb=" N LYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.871A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.181A pdb=" N ILE C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 216 through 226 removed outlier: 3.973A pdb=" N TYR C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 255 removed outlier: 4.125A pdb=" N THR C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 316 removed outlier: 3.794A pdb=" N VAL C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Proline residue: C 338 - end of helix Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.755A pdb=" N VAL C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.573A pdb=" N ILE C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 375 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 377 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 395 through 420 removed outlier: 4.403A pdb=" N LEU C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 433 Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.769A pdb=" N LYS C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.871A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 155 through 165 removed outlier: 4.088A pdb=" N ILE D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 removed outlier: 3.593A pdb=" N ARG D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.569A pdb=" N LYS D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.519A pdb=" N TYR D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 255 removed outlier: 3.648A pdb=" N ILE D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE D 250 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.634A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 348 removed outlier: 3.911A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 361 through 370 removed outlier: 4.073A pdb=" N VAL D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 372 No H-bonds generated for 'chain 'D' and resid 371 through 372' Processing helix chain 'D' and resid 373 through 377 removed outlier: 3.630A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 393 Processing helix chain 'D' and resid 395 through 420 removed outlier: 4.402A pdb=" N LEU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER D 414 " --> pdb=" O ILE D 410 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 433 Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.770A pdb=" N LYS D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.871A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.702A pdb=" N ARG H 66 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL H 67 " --> pdb=" O LYS H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 67' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.760A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 127 Processing helix chain 'H' and resid 127 through 133 Processing helix chain 'H' and resid 135 through 140 removed outlier: 3.658A pdb=" N CYS H 139 " --> pdb=" O CYS H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 241 No H-bonds generated for 'chain 'H' and resid 239 through 241' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.564A pdb=" N ASN L 31 " --> pdb=" O ASN L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.994A pdb=" N ASP L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 80 through 84' Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 3.504A pdb=" N VAL A 106 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 118 removed outlier: 3.672A pdb=" N ILE C 110 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 105 through 106 Processing sheet with id=AA5, first strand: chain 'D' and resid 113 through 114 removed outlier: 6.502A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.567A pdb=" N LEU H 12 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.567A pdb=" N LEU H 12 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER H 97 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS H 151 " --> pdb=" O HIS H 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 172 through 176 removed outlier: 3.649A pdb=" N LEU H 193 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 176 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS H 192 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP H 196 " --> pdb=" O TYR H 228 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR H 228 " --> pdb=" O ASP H 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 172 through 176 removed outlier: 3.649A pdb=" N LEU H 193 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 176 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS H 192 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP H 196 " --> pdb=" O TYR H 228 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR H 228 " --> pdb=" O ASP H 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 246 through 252 removed outlier: 4.174A pdb=" N TYR H 246 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS H 248 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS H 261 " --> pdb=" O CYS H 248 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL H 250 " --> pdb=" O VAL H 259 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 259 " --> pdb=" O VAL H 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.721A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU L 110 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY L 12 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR L 88 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.721A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU L 110 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY L 12 " --> pdb=" O LEU L 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.888A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.888A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.551A pdb=" N ALA L 134 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU L 136 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU L 182 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER L 179 " --> pdb=" O THR L 167 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR L 167 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR L 181 " --> pdb=" O THR L 165 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR L 165 " --> pdb=" O TYR L 181 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER L 183 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL L 163 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 149 through 150 removed outlier: 4.143A pdb=" N THR L 149 " --> pdb=" O THR L 200 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR L 200 " --> pdb=" O THR L 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 157 through 159 removed outlier: 3.687A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2094 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: 4.26 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2252 1.31 - 1.44: 3937 1.44 - 1.57: 7840 1.57 - 1.70: 0 1.70 - 1.84: 76 Bond restraints: 14105 Sorted by residual: bond pdb=" CA ARG B 370 " pdb=" C ARG B 370 " ideal model delta sigma weight residual 1.522 1.410 0.112 1.38e-02 5.25e+03 6.62e+01 bond pdb=" C SER D 394 " pdb=" N MET D 395 " ideal model delta sigma weight residual 1.335 1.244 0.091 1.38e-02 5.25e+03 4.32e+01 bond pdb=" CA CYS H 119 " pdb=" C CYS H 119 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.32e-02 5.74e+03 2.75e+01 bond pdb=" C ARG B 370 " pdb=" O ARG B 370 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.29e-02 6.01e+03 2.25e+01 bond pdb=" CA SER D 413 " pdb=" CB SER D 413 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.56e-02 4.11e+03 2.05e+01 ... (remaining 14100 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.96: 354 104.96 - 112.42: 6399 112.42 - 119.88: 6494 119.88 - 127.34: 5828 127.34 - 134.80: 101 Bond angle restraints: 19176 Sorted by residual: angle pdb=" CA PHE H 198 " pdb=" C PHE H 198 " pdb=" O PHE H 198 " ideal model delta sigma weight residual 120.28 110.45 9.83 1.03e+00 9.43e-01 9.11e+01 angle pdb=" CA PHE H 198 " pdb=" C PHE H 198 " pdb=" N PRO H 199 " ideal model delta sigma weight residual 117.75 126.67 -8.92 1.17e+00 7.31e-01 5.81e+01 angle pdb=" C CYS H 135 " pdb=" CA CYS H 135 " pdb=" CB CYS H 135 " ideal model delta sigma weight residual 111.85 100.81 11.04 1.47e+00 4.63e-01 5.64e+01 angle pdb=" CA ASP B 423 " pdb=" C ASP B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 117.82 123.26 -5.44 7.80e-01 1.64e+00 4.86e+01 angle pdb=" CA ASP A 423 " pdb=" C ASP A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 117.82 123.24 -5.42 7.80e-01 1.64e+00 4.82e+01 ... (remaining 19171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7452 17.25 - 34.49: 661 34.49 - 51.74: 157 51.74 - 68.99: 40 68.99 - 86.23: 11 Dihedral angle restraints: 8321 sinusoidal: 2908 harmonic: 5413 Sorted by residual: dihedral pdb=" CB CYS H 110 " pdb=" SG CYS H 110 " pdb=" SG CYS H 142 " pdb=" CB CYS H 142 " ideal model delta sinusoidal sigma weight residual -86.00 -163.60 77.60 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CB CYS H 124 " pdb=" SG CYS H 124 " pdb=" SG CYS H 139 " pdb=" CB CYS H 139 " ideal model delta sinusoidal sigma weight residual 93.00 163.91 -70.91 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" C THR C 444 " pdb=" N THR C 444 " pdb=" CA THR C 444 " pdb=" CB THR C 444 " ideal model delta harmonic sigma weight residual -122.00 -137.00 15.00 0 2.50e+00 1.60e-01 3.60e+01 ... (remaining 8318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1666 0.115 - 0.229: 464 0.229 - 0.344: 73 0.344 - 0.459: 9 0.459 - 0.573: 4 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CA THR C 444 " pdb=" N THR C 444 " pdb=" C THR C 444 " pdb=" CB THR C 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.57 2.00e-01 2.50e+01 8.21e+00 chirality pdb=" CA THR D 444 " pdb=" N THR D 444 " pdb=" C THR D 444 " pdb=" CB THR D 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA THR A 444 " pdb=" N THR A 444 " pdb=" C THR A 444 " pdb=" CB THR A 444 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.57 2.00e-01 2.50e+01 8.15e+00 ... (remaining 2213 not shown) Planarity restraints: 2481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 222 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C LEU A 222 " -0.076 2.00e-02 2.50e+03 pdb=" O LEU A 222 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 223 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 467 " -0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ALA B 467 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA B 467 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY B 468 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 467 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ALA A 467 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA A 467 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY A 468 " -0.022 2.00e-02 2.50e+03 ... (remaining 2478 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 3687 2.80 - 3.38: 14437 3.38 - 3.97: 23297 3.97 - 4.55: 32134 4.55 - 5.14: 48384 Nonbonded interactions: 121939 Sorted by model distance: nonbonded pdb=" O THR A 255 " pdb=" OG1 THR A 255 " model vdw 2.215 2.440 nonbonded pdb=" O THR B 255 " pdb=" OG1 THR B 255 " model vdw 2.251 2.440 nonbonded pdb=" OD1 ASP D 332 " pdb=" NZ LYS D 376 " model vdw 2.282 2.520 nonbonded pdb=" N ASP C 178 " pdb=" OD1 ASP C 178 " model vdw 2.288 2.520 nonbonded pdb=" NH2 ARG C 170 " pdb=" OD2 ASP D 178 " model vdw 2.312 2.520 ... (remaining 121934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 491) selection = chain 'B' selection = (chain 'C' and resid 103 through 491) selection = chain 'D' } 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: 4.490 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: 17.960 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.920 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 0.018 0.183 14105 Z= 1.121 Angle : 1.720 12.153 19176 Z= 1.198 Chirality : 0.108 0.573 2216 Planarity : 0.009 0.087 2481 Dihedral : 14.839 86.233 4806 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 6.26 % Allowed : 12.29 % Favored : 81.44 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.17), residues: 1842 helix: -1.79 (0.15), residues: 943 sheet: -2.46 (0.35), residues: 156 loop : -2.35 (0.19), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 221 HIS 0.013 0.004 HIS A 451 PHE 0.048 0.003 PHE H 122 TYR 0.023 0.003 TYR C 163 ARG 0.008 0.001 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 227 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7949 (mt0) cc_final: 0.6972 (mt0) REVERT: A 308 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7268 (t80) REVERT: A 392 LYS cc_start: 0.8669 (tttp) cc_final: 0.7975 (ttmm) REVERT: A 397 GLU cc_start: 0.8228 (mp0) cc_final: 0.7628 (mt-10) REVERT: A 422 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6839 (p0) REVERT: A 489 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7580 (tmm-80) REVERT: B 205 ARG cc_start: 0.6551 (mtt180) cc_final: 0.6324 (tpp-160) REVERT: B 210 PRO cc_start: 0.7624 (Cg_endo) cc_final: 0.7335 (Cg_exo) REVERT: B 367 ARG cc_start: 0.8281 (mpt180) cc_final: 0.7774 (mmm160) REVERT: B 405 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8451 (mt) REVERT: C 209 ARG cc_start: 0.7449 (pmt170) cc_final: 0.7181 (ptt-90) REVERT: C 405 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8172 (mp) REVERT: D 424 PRO cc_start: 0.6075 (Cg_exo) cc_final: 0.4999 (Cg_endo) outliers start: 80 outliers final: 20 residues processed: 282 average time/residue: 0.3114 time to fit residues: 119.6475 Evaluate side-chains 152 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 145 ASN A 164 GLN A 484 ASN C 124 GLN C 145 ASN C 385 GLN C 484 ASN D 484 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14105 Z= 0.245 Angle : 0.656 6.185 19176 Z= 0.355 Chirality : 0.044 0.206 2216 Planarity : 0.007 0.065 2481 Dihedral : 6.506 57.177 2076 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.70 % Allowed : 15.27 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 1842 helix: 0.07 (0.17), residues: 929 sheet: -1.87 (0.39), residues: 158 loop : -1.94 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS A 488 PHE 0.023 0.002 PHE C 140 TYR 0.013 0.002 TYR B 139 ARG 0.007 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 155 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.7582 (m-80) cc_final: 0.6982 (m-80) REVERT: A 382 LYS cc_start: 0.8017 (tptt) cc_final: 0.7744 (tptt) REVERT: A 392 LYS cc_start: 0.8602 (tttp) cc_final: 0.7895 (ttmm) REVERT: A 397 GLU cc_start: 0.7856 (mp0) cc_final: 0.7480 (mt-10) REVERT: A 470 LEU cc_start: 0.8229 (mp) cc_final: 0.7994 (mp) REVERT: A 489 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7249 (tmm-80) REVERT: B 153 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8234 (mtp180) REVERT: B 210 PRO cc_start: 0.7247 (Cg_endo) cc_final: 0.7007 (Cg_exo) REVERT: B 367 ARG cc_start: 0.8144 (mpt180) cc_final: 0.7687 (mtp180) REVERT: D 380 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.7969 (m-70) outliers start: 60 outliers final: 28 residues processed: 205 average time/residue: 0.2801 time to fit residues: 81.6478 Evaluate side-chains 160 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 170 optimal weight: 40.0000 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 164 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 14105 Z= 0.497 Angle : 0.716 6.632 19176 Z= 0.386 Chirality : 0.048 0.265 2216 Planarity : 0.006 0.067 2481 Dihedral : 5.522 56.880 2047 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.09 % Allowed : 16.99 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.19), residues: 1842 helix: 0.07 (0.17), residues: 969 sheet: -1.48 (0.38), residues: 180 loop : -2.03 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.006 0.002 HIS H 126 PHE 0.027 0.002 PHE B 308 TYR 0.020 0.002 TYR C 147 ARG 0.004 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 130 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 LYS cc_start: 0.8092 (tptt) cc_final: 0.7854 (tptt) REVERT: A 392 LYS cc_start: 0.8676 (tttp) cc_final: 0.7978 (ttmm) REVERT: A 397 GLU cc_start: 0.7911 (mp0) cc_final: 0.7503 (mt-10) REVERT: A 406 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.6938 (t80) REVERT: A 489 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7267 (tmm-80) REVERT: B 153 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8417 (mtp180) REVERT: C 192 GLU cc_start: 0.8206 (pm20) cc_final: 0.7731 (pp20) REVERT: D 194 MET cc_start: 0.8077 (tpp) cc_final: 0.7664 (tpp) REVERT: D 380 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.8080 (m-70) outliers start: 65 outliers final: 41 residues processed: 183 average time/residue: 0.2448 time to fit residues: 66.2812 Evaluate side-chains 163 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.0270 chunk 127 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 170 optimal weight: 50.0000 chunk 180 optimal weight: 40.0000 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN C 145 ASN C 164 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14105 Z= 0.211 Angle : 0.555 7.712 19176 Z= 0.296 Chirality : 0.042 0.143 2216 Planarity : 0.006 0.065 2481 Dihedral : 4.845 52.554 2040 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.60 % Allowed : 18.72 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1842 helix: 0.96 (0.18), residues: 929 sheet: -0.94 (0.42), residues: 165 loop : -1.72 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS C 451 PHE 0.024 0.001 PHE D 186 TYR 0.017 0.001 TYR C 161 ARG 0.005 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8617 (tttp) cc_final: 0.8023 (ttmt) REVERT: A 397 GLU cc_start: 0.7782 (mp0) cc_final: 0.7392 (mt-10) REVERT: A 489 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7143 (tmm-80) REVERT: C 192 GLU cc_start: 0.8191 (pm20) cc_final: 0.7825 (pp20) REVERT: C 299 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: D 194 MET cc_start: 0.8088 (tpp) cc_final: 0.7631 (tpp) REVERT: D 380 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8007 (m-70) outliers start: 46 outliers final: 31 residues processed: 172 average time/residue: 0.2500 time to fit residues: 63.3218 Evaluate side-chains 155 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 154 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN C 145 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14105 Z= 0.437 Angle : 0.647 6.391 19176 Z= 0.346 Chirality : 0.046 0.183 2216 Planarity : 0.006 0.069 2481 Dihedral : 4.590 47.959 2029 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.62 % Allowed : 18.40 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1842 helix: 0.53 (0.17), residues: 969 sheet: -0.72 (0.42), residues: 160 loop : -1.80 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 436 HIS 0.005 0.001 HIS C 451 PHE 0.023 0.002 PHE C 406 TYR 0.016 0.002 TYR C 147 ARG 0.005 0.000 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 119 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8679 (tttp) cc_final: 0.7985 (ttmm) REVERT: A 397 GLU cc_start: 0.7833 (mp0) cc_final: 0.7422 (mt-10) REVERT: A 422 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7138 (p0) REVERT: A 489 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7231 (tmm-80) REVERT: C 121 THR cc_start: 0.8616 (p) cc_final: 0.8314 (t) REVERT: C 153 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7856 (ptm160) REVERT: C 299 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: D 194 MET cc_start: 0.8019 (tpp) cc_final: 0.7658 (tpp) REVERT: D 380 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8106 (m-70) outliers start: 59 outliers final: 42 residues processed: 170 average time/residue: 0.2509 time to fit residues: 63.5244 Evaluate side-chains 164 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 117 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.9980 chunk 162 optimal weight: 50.0000 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 180 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 15 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN B 145 ASN C 145 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14105 Z= 0.177 Angle : 0.532 6.796 19176 Z= 0.282 Chirality : 0.042 0.176 2216 Planarity : 0.005 0.070 2481 Dihedral : 4.279 45.027 2029 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.84 % Allowed : 19.97 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1842 helix: 1.28 (0.18), residues: 929 sheet: -0.93 (0.37), residues: 201 loop : -1.49 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS C 451 PHE 0.022 0.001 PHE D 186 TYR 0.017 0.001 TYR C 161 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 129 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8617 (tttp) cc_final: 0.8020 (ttmt) REVERT: A 397 GLU cc_start: 0.7791 (mp0) cc_final: 0.7382 (mt-10) REVERT: A 422 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7074 (p0) REVERT: A 489 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7106 (tmm-80) REVERT: B 484 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8168 (m-40) REVERT: C 120 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7776 (mmmt) REVERT: C 192 GLU cc_start: 0.8169 (pm20) cc_final: 0.7890 (pp20) REVERT: C 226 TYR cc_start: 0.7456 (m-80) cc_final: 0.7172 (m-80) REVERT: C 299 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: C 422 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6061 (p0) REVERT: D 337 ILE cc_start: 0.9248 (mm) cc_final: 0.9043 (mt) REVERT: D 380 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8002 (m-70) outliers start: 49 outliers final: 32 residues processed: 173 average time/residue: 0.2556 time to fit residues: 65.2839 Evaluate side-chains 157 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 chunk 109 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14105 Z= 0.168 Angle : 0.520 10.119 19176 Z= 0.273 Chirality : 0.041 0.211 2216 Planarity : 0.005 0.067 2481 Dihedral : 4.056 43.889 2029 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.45 % Allowed : 19.97 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1842 helix: 1.52 (0.18), residues: 929 sheet: -0.40 (0.41), residues: 170 loop : -1.47 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS C 451 PHE 0.020 0.001 PHE A 197 TYR 0.016 0.001 TYR C 161 ARG 0.010 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7349 (tpt170) REVERT: A 392 LYS cc_start: 0.8603 (tttp) cc_final: 0.7925 (ttmm) REVERT: A 397 GLU cc_start: 0.7770 (mp0) cc_final: 0.7285 (mt-10) REVERT: A 422 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7070 (p0) REVERT: A 489 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7055 (tmm-80) REVERT: C 120 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7518 (mmmt) REVERT: C 145 ASN cc_start: 0.7815 (t0) cc_final: 0.7567 (t0) REVERT: C 196 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8370 (ttmt) REVERT: C 299 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: D 380 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.8020 (m-70) outliers start: 44 outliers final: 31 residues processed: 166 average time/residue: 0.2409 time to fit residues: 60.3601 Evaluate side-chains 155 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 141 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3865 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: