Starting phenix.real_space_refine on Mon Apr 6 15:09:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5i_61142/04_2026/9j5i_61142.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5i_61142/04_2026/9j5i_61142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j5i_61142/04_2026/9j5i_61142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5i_61142/04_2026/9j5i_61142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j5i_61142/04_2026/9j5i_61142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5i_61142/04_2026/9j5i_61142.map" } resolution = 3.38 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= 0.001 sd= 0.101 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 Mn 4 7.51 5 S 66 5.16 5 C 12256 2.51 5 N 3310 2.21 5 O 3662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19298 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 3564 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 489, 3556 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 21, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 11, 'PHE:plan': 3, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 10, 'ASN:plan1': 3, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 489, 3556 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 21, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 11, 'PHE:plan': 3, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 10, 'ASN:plan1': 3, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 3617 Chain: "F" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 291, 2313 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 291, 2313 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 2358 Chain: "D" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 3762 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 901 Unresolved non-hydrogen dihedrals: 579 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 31, 'ASN:plan1': 6, 'ASP:plan': 17, 'GLN:plan1': 8, 'ARG:plan': 20, 'PHE:plan': 6, 'TYR:plan': 4, 'HIS:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "B" Number of atoms: 3564 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 489, 3556 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 21, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 11, 'PHE:plan': 3, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 10, 'ASN:plan1': 3, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 489, 3556 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 21, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 11, 'PHE:plan': 3, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 10, 'ASN:plan1': 3, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 3617 Chain: "C" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2313 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 3767 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Unresolved non-hydrogen bonds: 709 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 572 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 31, 'ASN:plan1': 6, 'ASP:plan': 17, 'GLN:plan1': 9, 'ARG:plan': 19, 'PHE:plan': 6, 'TYR:plan': 4, 'HIS:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 431 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASN E 398 " occ=0.58 ... (14 atoms not shown) pdb=" ND2BASN E 398 " occ=0.42 residue: pdb=" N AARG F 89 " occ=0.23 ... (20 atoms not shown) pdb=" NH2BARG F 89 " occ=0.77 residue: pdb=" N AASN B 398 " occ=0.64 ... (14 atoms not shown) pdb=" ND2BASN B 398 " occ=0.36 Time building chain proxies: 6.09, per 1000 atoms: 0.32 Number of scatterers: 19298 At special positions: 0 Unit cell: (161.2, 217.36, 131.04, 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) Mn 4 24.99 S 66 16.00 O 3662 8.00 N 3310 7.00 C 12256 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: 1.56 Conformation dependent library (CDL) restraints added in 964.6 milliseconds 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5154 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 10 sheets defined 75.0% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'E' and resid 180 through 188 Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 221 removed outlier: 3.647A pdb=" N GLN E 221 " --> pdb=" O PRO E 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 223 through 246 removed outlier: 8.349A pdb=" N ASP E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N SER E 235 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 250 through 269 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.617A pdb=" N THR E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 290 removed outlier: 3.624A pdb=" N ALA E 290 " --> pdb=" O ASP E 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 287 through 290' Processing helix chain 'E' and resid 291 through 308 removed outlier: 3.771A pdb=" N ASN E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 323 Processing helix chain 'E' and resid 324 through 338 removed outlier: 4.333A pdb=" N THR E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) Proline residue: E 330 - end of helix Processing helix chain 'E' and resid 341 through 359 Processing helix chain 'E' and resid 362 through 370 Processing helix chain 'E' and resid 378 through 381 removed outlier: 3.642A pdb=" N THR E 381 " --> pdb=" O ASP E 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 378 through 381' Processing helix chain 'E' and resid 382 through 396 removed outlier: 3.732A pdb=" N THR E 386 " --> pdb=" O ASN E 382 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN E 396 " --> pdb=" O THR E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 415 removed outlier: 3.614A pdb=" N VAL E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 431 removed outlier: 3.513A pdb=" N ILE E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 453 removed outlier: 3.533A pdb=" N ALA E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 453 " --> pdb=" O TRP E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'E' and resid 465 through 469 removed outlier: 3.704A pdb=" N VAL E 468 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY E 469 " --> pdb=" O GLU E 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 465 through 469' Processing helix chain 'E' and resid 477 through 492 Processing helix chain 'E' and resid 499 through 505 removed outlier: 4.198A pdb=" N LEU E 503 " --> pdb=" O MET E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 526 through 543 Processing helix chain 'E' and resid 546 through 554 Processing helix chain 'E' and resid 566 through 583 Processing helix chain 'E' and resid 589 through 598 removed outlier: 3.568A pdb=" N THR E 593 " --> pdb=" O LEU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 612 Processing helix chain 'E' and resid 616 through 634 Processing helix chain 'E' and resid 637 through 646 Processing helix chain 'E' and resid 651 through 669 Processing helix chain 'F' and resid 5 through 18 Processing helix chain 'F' and resid 24 through 42 Processing helix chain 'F' and resid 61 through 73 Processing helix chain 'F' and resid 92 through 107 removed outlier: 3.855A pdb=" N VAL F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 120 removed outlier: 4.039A pdb=" N SER F 120 " --> pdb=" O ASN F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.845A pdb=" N VAL F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 137 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 176 through 183 removed outlier: 3.900A pdb=" N ILE F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 201 removed outlier: 4.578A pdb=" N ASP F 197 " --> pdb=" O GLY F 193 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU F 199 " --> pdb=" O MET F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'D' and resid 13 through 19 removed outlier: 3.734A pdb=" N LYS D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 removed outlier: 3.714A pdb=" N ASN D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.680A pdb=" N ILE D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.570A pdb=" N ILE D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Proline residue: D 51 - end of helix Processing helix chain 'D' and resid 61 through 80 removed outlier: 3.606A pdb=" N VAL D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 4.267A pdb=" N GLY D 80 " --> pdb=" O PRO D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 96 Processing helix chain 'D' and resid 99 through 121 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 140 through 152 removed outlier: 4.269A pdb=" N SER D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 173 removed outlier: 4.095A pdb=" N THR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.798A pdb=" N ARG D 180 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 212 Processing helix chain 'D' and resid 217 through 230 Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 241 through 252 removed outlier: 3.680A pdb=" N VAL D 245 " --> pdb=" O HIS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 272 removed outlier: 4.131A pdb=" N TYR D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 290 removed outlier: 3.601A pdb=" N THR D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Proline residue: D 283 - end of helix removed outlier: 3.750A pdb=" N LEU D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 311 removed outlier: 3.567A pdb=" N ARG D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY D 302 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 330 removed outlier: 3.643A pdb=" N GLN D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Proline residue: D 322 - end of helix removed outlier: 4.024A pdb=" N ASP D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 351 removed outlier: 4.698A pdb=" N SER D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Proline residue: D 348 - end of helix Processing helix chain 'D' and resid 352 through 368 Proline residue: D 361 - end of helix removed outlier: 4.353A pdb=" N LYS D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.647A pdb=" N ARG D 375 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 407 removed outlier: 3.986A pdb=" N LEU D 394 " --> pdb=" O GLY D 390 " (cutoff:3.500A) Proline residue: D 400 - end of helix removed outlier: 3.575A pdb=" N GLU D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 429 Proline residue: D 422 - end of helix removed outlier: 3.646A pdb=" N GLN D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 449 through 468 Processing helix chain 'D' and resid 468 through 483 removed outlier: 4.721A pdb=" N VAL D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 492 through 506 Proline residue: D 504 - end of helix Processing helix chain 'D' and resid 508 through 524 Proline residue: D 517 - end of helix removed outlier: 3.963A pdb=" N LYS D 524 " --> pdb=" O MET D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 545 removed outlier: 3.636A pdb=" N LYS D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Proline residue: D 543 - end of helix Processing helix chain 'D' and resid 549 through 563 removed outlier: 3.649A pdb=" N THR D 553 " --> pdb=" O VAL D 549 " (cutoff:3.500A) Proline residue: D 556 - end of helix Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.512A pdb=" N SER D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 221 removed outlier: 3.649A pdb=" N GLN B 221 " --> pdb=" O PRO B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 223 through 246 removed outlier: 8.352A pdb=" N ASP B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N SER B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 269 Processing helix chain 'B' and resid 271 through 279 removed outlier: 3.642A pdb=" N THR B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 290 removed outlier: 3.622A pdb=" N ALA B 290 " --> pdb=" O ASP B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.772A pdb=" N ASN B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 324 through 338 removed outlier: 4.340A pdb=" N THR B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'B' and resid 341 through 359 Processing helix chain 'B' and resid 362 through 370 Processing helix chain 'B' and resid 378 through 381 removed outlier: 3.668A pdb=" N THR B 381 " --> pdb=" O ASP B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 382 through 396 removed outlier: 3.732A pdb=" N THR B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 415 removed outlier: 3.621A pdb=" N VAL B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 431 removed outlier: 3.515A pdb=" N ILE B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 453 removed outlier: 3.535A pdb=" N ALA B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 453 " --> pdb=" O TRP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.703A pdb=" N VAL B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY B 469 " --> pdb=" O GLU B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 469' Processing helix chain 'B' and resid 477 through 492 Processing helix chain 'B' and resid 499 through 505 removed outlier: 4.201A pdb=" N LEU B 503 " --> pdb=" O MET B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 526 through 543 Processing helix chain 'B' and resid 546 through 554 Processing helix chain 'B' and resid 566 through 583 Processing helix chain 'B' and resid 589 through 598 removed outlier: 3.587A pdb=" N THR B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 Processing helix chain 'B' and resid 616 through 634 Processing helix chain 'B' and resid 637 through 646 Processing helix chain 'B' and resid 651 through 669 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 24 through 42 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 removed outlier: 3.818A pdb=" N VAL C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 removed outlier: 4.037A pdb=" N SER C 120 " --> pdb=" O ASN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.860A pdb=" N VAL C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.887A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 4.579A pdb=" N ASP C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'A' and resid 13 through 19 removed outlier: 3.738A pdb=" N LYS A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.714A pdb=" N ASN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 41 removed outlier: 3.682A pdb=" N ILE A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 removed outlier: 4.568A pdb=" N ILE A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Proline residue: A 51 - end of helix Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.609A pdb=" N VAL A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 4.262A pdb=" N GLY A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 99 through 121 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 140 through 152 removed outlier: 4.270A pdb=" N SER A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 173 removed outlier: 4.095A pdb=" N THR A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.813A pdb=" N ARG A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 217 through 230 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 241 through 252 removed outlier: 3.714A pdb=" N VAL A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 272 removed outlier: 4.101A pdb=" N TYR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 289 removed outlier: 3.659A pdb=" N THR A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 293 through 311 removed outlier: 3.902A pdb=" N GLY A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 removed outlier: 3.675A pdb=" N GLN A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 4.032A pdb=" N ASP A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.719A pdb=" N SER A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 352 through 368 Proline residue: A 361 - end of helix removed outlier: 4.312A pdb=" N LYS A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.641A pdb=" N ARG A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.985A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Proline residue: A 400 - end of helix removed outlier: 3.583A pdb=" N GLU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 Proline residue: A 422 - end of helix removed outlier: 3.662A pdb=" N GLN A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 449 through 468 Processing helix chain 'A' and resid 468 through 483 removed outlier: 4.776A pdb=" N VAL A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 492 through 506 Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 508 through 524 Proline residue: A 517 - end of helix removed outlier: 3.958A pdb=" N LYS A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 545 removed outlier: 3.637A pdb=" N LYS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Proline residue: A 543 - end of helix Processing helix chain 'A' and resid 549 through 563 removed outlier: 3.613A pdb=" N THR A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Proline residue: A 556 - end of helix Processing helix chain 'A' and resid 566 through 582 removed outlier: 3.986A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.498A pdb=" N THR F 53 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 157 through 159 removed outlier: 3.619A pdb=" N ILE F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'F' and resid 249 through 250 removed outlier: 3.674A pdb=" N ASN F 249 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 273 through 274 removed outlier: 4.103A pdb=" N ALA F 273 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 289 " --> pdb=" O ALA F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.508A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 159 removed outlier: 3.617A pdb=" N ILE C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 210 through 211 Processing sheet with id=AA9, first strand: chain 'C' and resid 249 through 250 removed outlier: 3.675A pdb=" N ASN C 249 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 274 removed outlier: 4.109A pdb=" N ALA C 273 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 289 " --> pdb=" O ALA C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 1245 hydrogen bonds defined for protein. 3699 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: 2.85 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3559 1.33 - 1.45: 4653 1.45 - 1.57: 11350 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 19662 Sorted by residual: bond pdb=" C PHE C 289 " pdb=" N ASP C 290 " ideal model delta sigma weight residual 1.326 1.264 0.062 1.50e-02 4.44e+03 1.71e+01 bond pdb=" C PHE F 289 " pdb=" N ASP F 290 " ideal model delta sigma weight residual 1.331 1.264 0.067 2.07e-02 2.33e+03 1.04e+01 bond pdb=" C VAL B 568 " pdb=" N PHE B 569 " ideal model delta sigma weight residual 1.334 1.298 0.037 1.27e-02 6.20e+03 8.26e+00 bond pdb=" C VAL E 568 " pdb=" N PHE E 569 " ideal model delta sigma weight residual 1.334 1.299 0.035 1.27e-02 6.20e+03 7.70e+00 bond pdb=" N ASP E 325 " pdb=" CA ASP E 325 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.28e-02 6.10e+03 7.08e+00 ... (remaining 19657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 26563 2.83 - 5.66: 291 5.66 - 8.49: 54 8.49 - 11.32: 9 11.32 - 14.15: 11 Bond angle restraints: 26928 Sorted by residual: angle pdb=" O LEU B 564 " pdb=" C LEU B 564 " pdb=" N THR B 565 " ideal model delta sigma weight residual 121.64 134.02 -12.38 1.23e+00 6.61e-01 1.01e+02 angle pdb=" CA LEU B 564 " pdb=" C LEU B 564 " pdb=" N THR B 565 " ideal model delta sigma weight residual 119.80 106.97 12.83 1.34e+00 5.57e-01 9.17e+01 angle pdb=" O LEU E 564 " pdb=" C LEU E 564 " pdb=" N THR E 565 " ideal model delta sigma weight residual 122.59 134.45 -11.86 1.33e+00 5.65e-01 7.95e+01 angle pdb=" C GLU B 647 " pdb=" CA GLU B 647 " pdb=" CB GLU B 647 " ideal model delta sigma weight residual 109.55 95.82 13.73 1.68e+00 3.54e-01 6.68e+01 angle pdb=" C GLU E 647 " pdb=" CA GLU E 647 " pdb=" CB GLU E 647 " ideal model delta sigma weight residual 109.55 96.36 13.19 1.68e+00 3.54e-01 6.17e+01 ... (remaining 26923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10764 17.99 - 35.97: 775 35.97 - 53.96: 187 53.96 - 71.95: 31 71.95 - 89.93: 23 Dihedral angle restraints: 11780 sinusoidal: 3864 harmonic: 7916 Sorted by residual: dihedral pdb=" C ARG C 121 " pdb=" N ARG C 121 " pdb=" CA ARG C 121 " pdb=" CB ARG C 121 " ideal model delta harmonic sigma weight residual -122.60 -104.95 -17.65 0 2.50e+00 1.60e-01 4.98e+01 dihedral pdb=" C GLU B 647 " pdb=" N GLU B 647 " pdb=" CA GLU B 647 " pdb=" CB GLU B 647 " ideal model delta harmonic sigma weight residual -122.60 -105.40 -17.20 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C ARG F 121 " pdb=" N ARG F 121 " pdb=" CA ARG F 121 " pdb=" CB ARG F 121 " ideal model delta harmonic sigma weight residual -122.60 -105.56 -17.04 0 2.50e+00 1.60e-01 4.65e+01 ... (remaining 11777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3013 0.077 - 0.154: 214 0.154 - 0.231: 11 0.231 - 0.308: 4 0.308 - 0.385: 6 Chirality restraints: 3248 Sorted by residual: chirality pdb=" CA ARG C 121 " pdb=" N ARG C 121 " pdb=" C ARG C 121 " pdb=" CB ARG C 121 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ARG F 121 " pdb=" N ARG F 121 " pdb=" C ARG F 121 " pdb=" CB ARG F 121 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASN D 386 " pdb=" N ASN D 386 " pdb=" C ASN D 386 " pdb=" CB ASN D 386 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 3245 not shown) Planarity restraints: 3510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 121 " -0.903 9.50e-02 1.11e+02 4.05e-01 9.93e+01 pdb=" NE ARG F 121 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG F 121 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG F 121 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG F 121 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 444 " -0.039 2.00e-02 2.50e+03 3.54e-02 3.13e+01 pdb=" CG TRP A 444 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP A 444 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 444 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 444 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 444 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 444 " 0.039 2.00e-02 2.50e+03 3.52e-02 3.10e+01 pdb=" CG TRP D 444 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP D 444 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP D 444 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 444 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 444 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 444 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 444 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 444 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 444 " -0.001 2.00e-02 2.50e+03 ... (remaining 3507 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 482 2.70 - 3.25: 20434 3.25 - 3.80: 31478 3.80 - 4.35: 38076 4.35 - 4.90: 63070 Nonbonded interactions: 153540 Sorted by model distance: nonbonded pdb=" N ASP C 85 " pdb=" OD1 ASP C 85 " model vdw 2.149 3.120 nonbonded pdb=" N ASP F 85 " pdb=" OD1 ASP F 85 " model vdw 2.150 3.120 nonbonded pdb=" NH1 ARG C 121 " pdb=" OE1 GLU C 188 " model vdw 2.190 3.120 nonbonded pdb=" OD1 ASN C 117 " pdb="MN MN C 401 " model vdw 2.200 2.320 nonbonded pdb=" OD1 ASN F 117 " pdb="MN MN F 401 " model vdw 2.201 2.320 ... (remaining 153535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 289 or (resid 290 through 301 and (name N or na \ me CA or name C or name O or name CB )) or resid 302 through 318 or (resid 319 a \ nd (name N or name CA or name C or name O or name CB )) or resid 320 through 582 \ )) selection = (chain 'D' and (resid 12 through 334 or (resid 335 through 336 and (name N or na \ me CA or name C or name O or name CB )) or resid 337 through 383 or (resid 384 a \ nd (name N or name CA or name C or name O or name CB )) or resid 385 through 582 \ )) } ncs_group { reference = (chain 'B' and (resid 180 through 397 or resid 399 through 670)) selection = (chain 'E' and (resid 180 through 397 or resid 399 through 670)) } ncs_group { reference = (chain 'C' and (resid 4 through 88 or resid 90 through 402)) selection = (chain 'F' and (resid 4 through 88 or resid 90 through 402)) } 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=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19662 Z= 0.192 Angle : 0.782 14.149 26928 Z= 0.458 Chirality : 0.044 0.385 3248 Planarity : 0.010 0.405 3510 Dihedral : 14.565 89.934 6626 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.35 % Allowed : 14.52 % Favored : 83.14 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2687 helix: 1.38 (0.13), residues: 1840 sheet: -5.82 (0.66), residues: 20 loop : -2.31 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 290 TYR 0.019 0.001 TYR D 489 PHE 0.019 0.001 PHE A 532 TRP 0.098 0.002 TRP A 444 HIS 0.008 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00335 (19662) covalent geometry : angle 0.78218 (26928) hydrogen bonds : bond 0.12392 ( 1245) hydrogen bonds : angle 5.25383 ( 3699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: E 298 MET cc_start: 0.6792 (mmt) cc_final: 0.6424 (mmm) REVERT: E 365 GLU cc_start: 0.9014 (tt0) cc_final: 0.8776 (pt0) REVERT: E 544 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7965 (mttp) REVERT: E 647 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: F 113 ILE cc_start: 0.8780 (mm) cc_final: 0.8557 (mt) REVERT: F 280 ASP cc_start: 0.7464 (m-30) cc_final: 0.7089 (m-30) REVERT: D 568 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6529 (t0) REVERT: B 298 MET cc_start: 0.6798 (mmt) cc_final: 0.6445 (mmm) REVERT: B 647 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: C 89 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7036 (mtt90) REVERT: C 113 ILE cc_start: 0.8815 (mm) cc_final: 0.8572 (mt) REVERT: C 280 ASP cc_start: 0.7430 (m-30) cc_final: 0.7053 (m-30) REVERT: A 258 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6802 (mpp80) REVERT: A 568 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6286 (t0) outliers start: 40 outliers final: 30 residues processed: 195 average time/residue: 0.1166 time to fit residues: 37.9262 Evaluate side-chains 187 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 544 LYS Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 640 GLN Chi-restraints excluded: chain E residue 647 GLU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 568 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.0770 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 462 ASN F 27 GLN C 27 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.163591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126943 restraints weight = 84329.697| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 5.25 r_work: 0.3725 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19662 Z= 0.121 Angle : 0.585 9.067 26928 Z= 0.301 Chirality : 0.039 0.156 3248 Planarity : 0.005 0.079 3510 Dihedral : 6.239 57.397 2909 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.46 % Allowed : 15.19 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2687 helix: 1.51 (0.13), residues: 1856 sheet: -5.79 (0.68), residues: 20 loop : -2.21 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 420 TYR 0.017 0.001 TYR B 553 PHE 0.015 0.001 PHE D 532 TRP 0.062 0.002 TRP A 444 HIS 0.006 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00253 (19662) covalent geometry : angle 0.58481 (26928) hydrogen bonds : bond 0.03589 ( 1245) hydrogen bonds : angle 4.19345 ( 3699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: E 298 MET cc_start: 0.6871 (mmt) cc_final: 0.6621 (mmm) REVERT: E 365 GLU cc_start: 0.8902 (tt0) cc_final: 0.8698 (tt0) REVERT: F 113 ILE cc_start: 0.8844 (mm) cc_final: 0.8612 (mt) REVERT: B 298 MET cc_start: 0.6855 (mmt) cc_final: 0.6610 (mmm) REVERT: B 365 GLU cc_start: 0.8988 (tp30) cc_final: 0.8617 (tt0) REVERT: B 563 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8289 (tp) REVERT: C 113 ILE cc_start: 0.8848 (mm) cc_final: 0.8618 (mt) REVERT: C 204 ASP cc_start: 0.7241 (m-30) cc_final: 0.6991 (m-30) REVERT: A 568 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6429 (t0) outliers start: 42 outliers final: 24 residues processed: 206 average time/residue: 0.1136 time to fit residues: 39.2752 Evaluate side-chains 174 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 499 MET Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 568 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 232 optimal weight: 0.0870 chunk 193 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.163088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.123582 restraints weight = 73156.509| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 4.47 r_work: 0.3744 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19662 Z= 0.120 Angle : 0.582 9.162 26928 Z= 0.296 Chirality : 0.039 0.162 3248 Planarity : 0.005 0.068 3510 Dihedral : 4.980 45.360 2853 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.46 % Allowed : 16.36 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2687 helix: 1.57 (0.13), residues: 1854 sheet: -5.82 (0.63), residues: 20 loop : -2.14 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.016 0.001 TYR B 553 PHE 0.020 0.001 PHE A 532 TRP 0.069 0.001 TRP A 444 HIS 0.009 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00265 (19662) covalent geometry : angle 0.58171 (26928) hydrogen bonds : bond 0.03401 ( 1245) hydrogen bonds : angle 4.05659 ( 3699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: E 298 MET cc_start: 0.6894 (mmt) cc_final: 0.6688 (mmm) REVERT: E 365 GLU cc_start: 0.8791 (tt0) cc_final: 0.8575 (tt0) REVERT: F 113 ILE cc_start: 0.8867 (mm) cc_final: 0.8640 (mt) REVERT: B 421 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7861 (mm) REVERT: B 563 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8226 (tp) REVERT: C 113 ILE cc_start: 0.8883 (mm) cc_final: 0.8667 (mt) outliers start: 42 outliers final: 26 residues processed: 198 average time/residue: 0.1167 time to fit residues: 38.7301 Evaluate side-chains 185 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 449 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 153 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 209 optimal weight: 0.9980 chunk 232 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 54 optimal weight: 0.3980 chunk 137 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.161813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.121701 restraints weight = 82543.221| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 5.01 r_work: 0.3712 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19662 Z= 0.133 Angle : 0.594 9.699 26928 Z= 0.300 Chirality : 0.039 0.166 3248 Planarity : 0.005 0.061 3510 Dihedral : 4.812 47.914 2849 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.13 % Allowed : 16.64 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2687 helix: 1.65 (0.13), residues: 1846 sheet: -5.72 (0.68), residues: 20 loop : -2.20 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 135 TYR 0.017 0.001 TYR D 285 PHE 0.022 0.002 PHE A 532 TRP 0.077 0.002 TRP A 444 HIS 0.007 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00303 (19662) covalent geometry : angle 0.59417 (26928) hydrogen bonds : bond 0.03367 ( 1245) hydrogen bonds : angle 4.00082 ( 3699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: E 365 GLU cc_start: 0.8808 (tt0) cc_final: 0.8562 (tt0) REVERT: F 59 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.7803 (t70) REVERT: D 568 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6290 (t0) REVERT: B 421 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7846 (mm) REVERT: B 563 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8261 (tp) REVERT: C 59 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.7731 (t70) REVERT: C 131 ASP cc_start: 0.7775 (t70) cc_final: 0.7380 (t0) REVERT: A 525 ASP cc_start: 0.6120 (t0) cc_final: 0.5912 (t0) outliers start: 54 outliers final: 28 residues processed: 208 average time/residue: 0.1253 time to fit residues: 43.0760 Evaluate side-chains 179 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 38 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 175 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.162140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.121736 restraints weight = 104629.117| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 6.09 r_work: 0.3671 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19662 Z= 0.123 Angle : 0.585 10.521 26928 Z= 0.295 Chirality : 0.039 0.167 3248 Planarity : 0.005 0.068 3510 Dihedral : 4.584 47.700 2843 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.79 % Allowed : 17.76 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2687 helix: 1.67 (0.13), residues: 1848 sheet: -5.62 (0.70), residues: 20 loop : -2.16 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.016 0.001 TYR A 285 PHE 0.021 0.001 PHE A 532 TRP 0.079 0.002 TRP A 444 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00276 (19662) covalent geometry : angle 0.58509 (26928) hydrogen bonds : bond 0.03255 ( 1245) hydrogen bonds : angle 3.95425 ( 3699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: E 365 GLU cc_start: 0.8780 (tt0) cc_final: 0.8575 (tt0) REVERT: F 188 GLU cc_start: 0.7288 (tp30) cc_final: 0.7059 (mm-30) REVERT: B 421 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7810 (mm) REVERT: B 563 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8263 (tp) outliers start: 48 outliers final: 32 residues processed: 205 average time/residue: 0.1206 time to fit residues: 40.9673 Evaluate side-chains 186 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 222 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 120 optimal weight: 0.0970 chunk 219 optimal weight: 20.0000 chunk 177 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 36 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 HIS ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.163141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.123270 restraints weight = 98994.348| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 5.94 r_work: 0.3698 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19662 Z= 0.113 Angle : 0.574 10.882 26928 Z= 0.288 Chirality : 0.038 0.169 3248 Planarity : 0.005 0.064 3510 Dihedral : 4.520 47.978 2843 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.29 % Allowed : 18.20 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2687 helix: 1.75 (0.13), residues: 1848 sheet: -3.65 (0.78), residues: 34 loop : -2.16 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.014 0.001 TYR A 285 PHE 0.020 0.001 PHE A 532 TRP 0.079 0.002 TRP A 444 HIS 0.006 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00250 (19662) covalent geometry : angle 0.57369 (26928) hydrogen bonds : bond 0.03103 ( 1245) hydrogen bonds : angle 3.89183 ( 3699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 163 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: E 298 MET cc_start: 0.7315 (mmm) cc_final: 0.6650 (mmm) REVERT: F 59 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8425 (t70) REVERT: F 188 GLU cc_start: 0.7234 (tp30) cc_final: 0.6974 (mm-30) REVERT: D 112 ARG cc_start: 0.6328 (mtm-85) cc_final: 0.4945 (tpp-160) REVERT: D 490 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7974 (mt) REVERT: B 421 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7693 (mm) REVERT: B 563 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8187 (tp) REVERT: A 490 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7998 (mt) outliers start: 57 outliers final: 32 residues processed: 212 average time/residue: 0.1224 time to fit residues: 42.4645 Evaluate side-chains 186 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 CYS Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 505 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 204 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 241 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.156735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.116563 restraints weight = 74216.169| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 4.45 r_work: 0.3617 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19662 Z= 0.234 Angle : 0.686 11.654 26928 Z= 0.351 Chirality : 0.043 0.204 3248 Planarity : 0.005 0.065 3510 Dihedral : 4.820 44.239 2841 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.02 % Allowed : 19.15 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2687 helix: 1.55 (0.13), residues: 1850 sheet: -4.14 (0.79), residues: 30 loop : -2.38 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 239 TYR 0.023 0.002 TYR A 285 PHE 0.028 0.002 PHE A 532 TRP 0.057 0.002 TRP A 444 HIS 0.033 0.002 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00549 (19662) covalent geometry : angle 0.68611 (26928) hydrogen bonds : bond 0.03970 ( 1245) hydrogen bonds : angle 4.11103 ( 3699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: F 59 HIS cc_start: 0.9141 (OUTLIER) cc_final: 0.8098 (t-90) REVERT: D 112 ARG cc_start: 0.6588 (mtm-85) cc_final: 0.5117 (tpp-160) REVERT: D 475 HIS cc_start: 0.7259 (t-170) cc_final: 0.7024 (t-170) REVERT: D 568 ASP cc_start: 0.6770 (OUTLIER) cc_final: 0.6478 (t0) REVERT: B 421 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7949 (mm) REVERT: B 486 GLU cc_start: 0.8062 (tp30) cc_final: 0.7743 (tp30) REVERT: C 188 GLU cc_start: 0.7658 (tp30) cc_final: 0.7396 (tp30) REVERT: A 112 ARG cc_start: 0.6423 (mtm-85) cc_final: 0.5051 (tpp-160) REVERT: A 475 HIS cc_start: 0.7117 (t-170) cc_final: 0.6886 (t-170) outliers start: 52 outliers final: 34 residues processed: 198 average time/residue: 0.1206 time to fit residues: 39.1584 Evaluate side-chains 181 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 563 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 219 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 192 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 240 optimal weight: 6.9990 chunk 248 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.160727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.120156 restraints weight = 98835.017| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 5.96 r_work: 0.3647 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19662 Z= 0.123 Angle : 0.603 11.665 26928 Z= 0.303 Chirality : 0.039 0.173 3248 Planarity : 0.005 0.066 3510 Dihedral : 4.598 45.741 2841 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.07 % Allowed : 21.05 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2687 helix: 1.71 (0.13), residues: 1844 sheet: -4.06 (0.82), residues: 30 loop : -2.26 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 121 TYR 0.014 0.001 TYR A 285 PHE 0.021 0.001 PHE A 532 TRP 0.056 0.001 TRP A 444 HIS 0.008 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00275 (19662) covalent geometry : angle 0.60300 (26928) hydrogen bonds : bond 0.03318 ( 1245) hydrogen bonds : angle 3.94903 ( 3699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: E 298 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.6253 (mmm) REVERT: D 112 ARG cc_start: 0.6430 (mtm-85) cc_final: 0.5049 (tpp-160) REVERT: D 475 HIS cc_start: 0.7216 (t-170) cc_final: 0.6989 (t-170) REVERT: B 421 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7807 (mm) REVERT: C 188 GLU cc_start: 0.7525 (tp30) cc_final: 0.7310 (tp30) REVERT: A 112 ARG cc_start: 0.6374 (mtm-85) cc_final: 0.5085 (tpp-160) REVERT: A 490 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8159 (mt) outliers start: 35 outliers final: 28 residues processed: 184 average time/residue: 0.1216 time to fit residues: 36.7994 Evaluate side-chains 175 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 563 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 111 optimal weight: 0.7980 chunk 186 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 167 optimal weight: 0.0010 chunk 151 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 161 optimal weight: 0.0870 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.162438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.122755 restraints weight = 93164.320| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 5.79 r_work: 0.3697 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19662 Z= 0.115 Angle : 0.597 11.678 26928 Z= 0.299 Chirality : 0.039 0.179 3248 Planarity : 0.005 0.067 3510 Dihedral : 4.474 46.782 2841 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.12 % Allowed : 20.83 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.17), residues: 2687 helix: 1.76 (0.13), residues: 1840 sheet: -4.06 (0.83), residues: 30 loop : -2.20 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 121 TYR 0.013 0.001 TYR A 285 PHE 0.020 0.001 PHE A 532 TRP 0.088 0.002 TRP A 444 HIS 0.005 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00251 (19662) covalent geometry : angle 0.59676 (26928) hydrogen bonds : bond 0.03162 ( 1245) hydrogen bonds : angle 3.89043 ( 3699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: E 298 MET cc_start: 0.6647 (mmt) cc_final: 0.6362 (mmm) REVERT: E 421 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7785 (mm) REVERT: D 112 ARG cc_start: 0.6378 (mtm-85) cc_final: 0.4979 (tpp-160) REVERT: D 490 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8096 (mt) REVERT: B 298 MET cc_start: 0.7292 (mmm) cc_final: 0.6608 (mmm) REVERT: B 421 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7739 (mm) REVERT: C 188 GLU cc_start: 0.7485 (tp30) cc_final: 0.7269 (tp30) REVERT: A 112 ARG cc_start: 0.6318 (mtm-85) cc_final: 0.4989 (tpp-160) REVERT: A 490 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8133 (mt) outliers start: 36 outliers final: 27 residues processed: 182 average time/residue: 0.1184 time to fit residues: 35.7672 Evaluate side-chains 178 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 563 ILE Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 264 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 97 optimal weight: 0.0070 chunk 180 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.159513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.118979 restraints weight = 98747.209| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 5.77 r_work: 0.3625 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19662 Z= 0.157 Angle : 0.630 11.737 26928 Z= 0.316 Chirality : 0.041 0.175 3248 Planarity : 0.005 0.068 3510 Dihedral : 4.562 45.430 2841 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.95 % Allowed : 21.05 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2687 helix: 1.72 (0.13), residues: 1844 sheet: -4.15 (0.80), residues: 30 loop : -2.26 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 492 TYR 0.017 0.002 TYR A 285 PHE 0.023 0.002 PHE A 532 TRP 0.083 0.002 TRP A 444 HIS 0.008 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00368 (19662) covalent geometry : angle 0.62993 (26928) hydrogen bonds : bond 0.03431 ( 1245) hydrogen bonds : angle 3.93812 ( 3699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: D 112 ARG cc_start: 0.6348 (mtm-85) cc_final: 0.4975 (tpp-160) REVERT: B 421 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7842 (mm) REVERT: C 188 GLU cc_start: 0.7639 (tp30) cc_final: 0.7381 (tp30) REVERT: A 112 ARG cc_start: 0.6314 (mtm-85) cc_final: 0.4997 (tpp-160) outliers start: 33 outliers final: 29 residues processed: 174 average time/residue: 0.1177 time to fit residues: 33.8664 Evaluate side-chains 173 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 94 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 211 optimal weight: 0.0770 chunk 99 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 229 optimal weight: 5.9990 overall best weight: 3.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.153004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.114126 restraints weight = 72432.987| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 4.50 r_work: 0.3521 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 19662 Z= 0.331 Angle : 0.794 12.791 26928 Z= 0.409 Chirality : 0.048 0.219 3248 Planarity : 0.006 0.067 3510 Dihedral : 5.285 41.001 2841 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.18 % Allowed : 20.88 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2687 helix: 1.18 (0.12), residues: 1854 sheet: None (None), residues: 0 loop : -2.76 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 239 TYR 0.026 0.003 TYR A 285 PHE 0.027 0.003 PHE A 532 TRP 0.083 0.003 TRP A 444 HIS 0.011 0.002 HIS F 191 Details of bonding type rmsd covalent geometry : bond 0.00784 (19662) covalent geometry : angle 0.79411 (26928) hydrogen bonds : bond 0.04712 ( 1245) hydrogen bonds : angle 4.49775 ( 3699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6051.94 seconds wall clock time: 103 minutes 50.25 seconds (6230.25 seconds total)