Starting phenix.real_space_refine on Sat Jul 4 09:40:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5i_61142/07_2026/9j5i_61142.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5i_61142/07_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_61142/07_2026/9j5i_61142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5i_61142/07_2026/9j5i_61142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j5i_61142/07_2026/9j5i_61142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5i_61142/07_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 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: 5.81, per 1000 atoms: 0.30 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: 1.67 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.57 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: 3.49 Time building geometry restraints manager: 2.23 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 3.060 nonbonded pdb=" OD1 ASN F 117 " pdb="MN MN F 401 " model vdw 2.201 3.060 ... (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: 3.140 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.810 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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/Z covalent geometry : bond 0.00335 / 0.19 (19662) covalent geometry : angle 0.78218 / 0.46 (26928) hydrogen bonds : bond 0.12392 / 8.63 ( 1245) hydrogen bonds : angle 5.25383 / 3.81 ( 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 : 0.757 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: 0.1245 time to fit residues: 40.1763 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 : 0.772 ------------------------------------------------------------------------------- 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... E 462 ASN F 27 GLN C 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.163665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.125958 restraints weight = 84283.153| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 5.04 r_work: 0.3738 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0773 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= 0.120 Angle : 0.587 9.109 26928 Z= 0.302 Chirality : 0.039 0.162 3248 Planarity : 0.005 0.078 3510 Dihedral : 6.233 57.454 2909 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.40 % Allowed : 15.24 % 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: 1.50 (0.13), residues: 1856 sheet: -5.74 (0.67), residues: 20 loop : -2.20 (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 0.018 0.001 PHE D 532 TRP 0.060 0.002 TRP A 444 HIS 0.006 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (19662) covalent geometry : angle 0.58677 / 0.30 (26928) hydrogen bonds : bond 0.03563 / 2.50 ( 1245) hydrogen bonds : angle 4.19954 / 3.05 ( 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 208 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: E 298 MET cc_start: 0.6872 (mmt) cc_final: 0.6623 (mmm) REVERT: E 365 GLU cc_start: 0.8869 (tt0) cc_final: 0.8659 (tt0) REVERT: F 113 ILE cc_start: 0.8848 (mm) cc_final: 0.8617 (mt) REVERT: B 298 MET cc_start: 0.6860 (mmt) cc_final: 0.6612 (mmm) REVERT: B 365 GLU cc_start: 0.8972 (tp30) cc_final: 0.8609 (tt0) REVERT: C 113 ILE cc_start: 0.8856 (mm) cc_final: 0.8626 (mt) REVERT: A 568 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6391 (t0) outliers start: 41 outliers final: 22 residues processed: 203 average time/residue: 0.1146 time to fit residues: 39.1968 Evaluate side-chains 172 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 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 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: 0.1980 chunk 193 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 59 HIS ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4499 r_free = 0.4499 target = 0.162607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.124422 restraints weight = 73237.254| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 4.65 r_work: 0.3746 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19662 Z= 0.127 Angle : 0.585 9.168 26928 Z= 0.298 Chirality : 0.039 0.165 3248 Planarity : 0.005 0.067 3510 Dihedral : 4.895 45.107 2849 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.29 % Allowed : 16.64 % Favored : 81.07 % 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: 0.66 (0.17), residues: 2687 helix: 1.56 (0.13), residues: 1854 sheet: -5.77 (0.61), residues: 20 loop : -2.13 (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 0.021 0.001 PHE A 532 TRP 0.070 0.002 TRP A 444 HIS 0.007 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19662) covalent geometry : angle 0.58540 / 0.30 (26928) hydrogen bonds : bond 0.03445 / 2.41 ( 1245) hydrogen bonds : angle 4.07628 / 2.96 ( 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 202 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: E 298 MET cc_start: 0.6926 (mmt) cc_final: 0.6708 (mmm) REVERT: F 59 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8019 (t70) REVERT: F 113 ILE cc_start: 0.8892 (mm) cc_final: 0.8672 (mt) REVERT: D 568 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.6297 (t0) REVERT: B 298 MET cc_start: 0.6895 (mmt) cc_final: 0.6679 (mmm) REVERT: B 421 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7928 (mm) REVERT: B 563 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8230 (tp) REVERT: C 113 ILE cc_start: 0.8914 (mm) cc_final: 0.8697 (mt) outliers start: 39 outliers final: 26 residues processed: 193 average time/residue: 0.1056 time to fit residues: 34.1041 Evaluate side-chains 175 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 398 LEU Chi-restraints excluded: chain D residue 449 VAL 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 142 VAL Chi-restraints excluded: chain C residue 170 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 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: 6.9990 chunk 80 optimal weight: 40.0000 chunk 209 optimal weight: 0.1980 chunk 232 optimal weight: 0.0470 chunk 155 optimal weight: 0.0670 chunk 183 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 210 optimal weight: 0.0870 chunk 54 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 59 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.164906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.126725 restraints weight = 84773.067| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 5.39 r_work: 0.3763 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19662 Z= 0.111 Angle : 0.573 9.616 26928 Z= 0.289 Chirality : 0.038 0.177 3248 Planarity : 0.005 0.060 3510 Dihedral : 4.678 48.383 2847 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.46 % Allowed : 16.86 % Favored : 80.68 % 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: 0.74 (0.17), residues: 2687 helix: 1.59 (0.13), residues: 1870 sheet: -5.62 (0.58), residues: 20 loop : -2.08 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 135 TYR 0.015 0.001 TYR B 553 PHE 0.019 0.001 PHE A 532 TRP 0.074 0.002 TRP A 444 HIS 0.015 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (19662) covalent geometry : angle 0.57268 / 0.29 (26928) hydrogen bonds : bond 0.03163 / 2.21 ( 1245) hydrogen bonds : angle 3.98644 / 2.90 ( 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 206 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: E 591 ILE cc_start: 0.8219 (pt) cc_final: 0.7947 (pt) REVERT: F 113 ILE cc_start: 0.8843 (mm) cc_final: 0.8611 (mt) REVERT: B 421 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7778 (mm) REVERT: B 486 GLU cc_start: 0.7882 (tp30) cc_final: 0.7594 (tp30) REVERT: B 563 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8203 (tp) REVERT: B 591 ILE cc_start: 0.8207 (pt) cc_final: 0.7933 (pt) REVERT: C 113 ILE cc_start: 0.8871 (mm) cc_final: 0.8647 (mt) REVERT: C 131 ASP cc_start: 0.7805 (t70) cc_final: 0.7422 (t0) REVERT: A 490 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7977 (mt) REVERT: A 525 ASP cc_start: 0.5933 (t0) cc_final: 0.5666 (t0) outliers start: 42 outliers final: 24 residues processed: 198 average time/residue: 0.1143 time to fit residues: 36.8789 Evaluate side-chains 178 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 59 HIS 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 549 VAL Chi-restraints excluded: chain B residue 378 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 50 CYS Chi-restraints excluded: chain C residue 58 VAL 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: 0.9990 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 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 = 0.4427 r_free = 0.4427 target = 0.156689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.118918 restraints weight = 103985.654| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 6.51 r_work: 0.3544 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19662 Z= 0.233 Angle : 0.692 11.316 26928 Z= 0.355 Chirality : 0.044 0.207 3248 Planarity : 0.005 0.066 3510 Dihedral : 4.982 49.237 2843 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.18 % Allowed : 18.09 % Favored : 78.73 % 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: 0.50 (0.17), residues: 2687 helix: 1.51 (0.13), residues: 1846 sheet: -4.39 (0.68), residues: 30 loop : -2.33 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 239 TYR 0.023 0.002 TYR A 285 PHE 0.028 0.002 PHE D 532 TRP 0.072 0.002 TRP A 444 HIS 0.009 0.002 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (19662) covalent geometry : angle 0.69217 / 0.36 (26928) hydrogen bonds : bond 0.04101 / 2.84 ( 1245) hydrogen bonds : angle 4.22635 / 3.07 ( 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 207 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: F 113 ILE cc_start: 0.8958 (mm) cc_final: 0.8746 (mt) REVERT: D 568 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6444 (t0) REVERT: B 486 GLU cc_start: 0.8191 (tp30) cc_final: 0.7546 (tp30) REVERT: C 131 ASP cc_start: 0.7859 (t70) cc_final: 0.7583 (t0) REVERT: A 475 HIS cc_start: 0.7216 (t-170) cc_final: 0.6946 (t70) REVERT: A 568 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6436 (t0) outliers start: 55 outliers final: 30 residues processed: 200 average time/residue: 0.1206 time to fit residues: 40.2734 Evaluate side-chains 173 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 59 HIS 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 449 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 549 VAL 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 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 71 ILE Chi-restraints excluded: chain C residue 96 THR 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 449 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 568 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 222 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 219 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 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 = 0.4468 r_free = 0.4468 target = 0.159941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.119573 restraints weight = 98344.250| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 5.94 r_work: 0.3632 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19662 Z= 0.133 Angle : 0.607 10.818 26928 Z= 0.307 Chirality : 0.039 0.169 3248 Planarity : 0.005 0.065 3510 Dihedral : 4.745 45.426 2841 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.68 % Allowed : 19.32 % Favored : 78.00 % 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: 0.63 (0.17), residues: 2687 helix: 1.60 (0.13), residues: 1852 sheet: -4.11 (0.77), residues: 30 loop : -2.31 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.015 0.001 TYR A 285 PHE 0.022 0.002 PHE A 532 TRP 0.058 0.001 TRP A 444 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (19662) covalent geometry : angle 0.60697 / 0.31 (26928) hydrogen bonds : bond 0.03471 / 2.43 ( 1245) hydrogen bonds : angle 4.02726 / 2.92 ( 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 199 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: F 113 ILE cc_start: 0.8892 (mm) cc_final: 0.8671 (mt) REVERT: F 188 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6644 (tm-30) REVERT: B 421 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7951 (mm) outliers start: 46 outliers final: 29 residues processed: 192 average time/residue: 0.1156 time to fit residues: 37.0230 Evaluate side-chains 175 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 E residue 563 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 50 CYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 204 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 497 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 = 0.4440 r_free = 0.4440 target = 0.157623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.118229 restraints weight = 74586.976| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 4.65 r_work: 0.3631 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19662 Z= 0.185 Angle : 0.643 11.029 26928 Z= 0.328 Chirality : 0.041 0.192 3248 Planarity : 0.005 0.065 3510 Dihedral : 4.841 48.740 2841 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.46 % Allowed : 20.32 % Favored : 77.22 % 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: 0.50 (0.17), residues: 2687 helix: 1.51 (0.13), residues: 1856 sheet: -4.28 (0.76), residues: 30 loop : -2.41 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 239 TYR 0.019 0.002 TYR A 285 PHE 0.026 0.002 PHE A 532 TRP 0.071 0.002 TRP A 444 HIS 0.006 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (19662) covalent geometry : angle 0.64270 / 0.33 (26928) hydrogen bonds : bond 0.03743 / 2.60 ( 1245) hydrogen bonds : angle 4.11633 / 2.98 ( 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 189 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: F 113 ILE cc_start: 0.8906 (mm) cc_final: 0.8699 (mt) REVERT: F 188 GLU cc_start: 0.7673 (mm-30) cc_final: 0.6793 (tm-30) REVERT: D 112 ARG cc_start: 0.6601 (mtm-85) cc_final: 0.5151 (tpp-160) REVERT: B 421 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8044 (mm) REVERT: C 188 GLU cc_start: 0.7703 (tp30) cc_final: 0.7332 (tp30) outliers start: 42 outliers final: 31 residues processed: 184 average time/residue: 0.1128 time to fit residues: 34.0985 Evaluate side-chains 177 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 449 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 58 VAL Chi-restraints excluded: chain C residue 71 ILE 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 449 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: 1.9990 chunk 26 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 68 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 497 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 = 0.4467 r_free = 0.4467 target = 0.159850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.119417 restraints weight = 96628.751| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 5.87 r_work: 0.3633 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1874 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= 0.132 Angle : 0.606 11.237 26928 Z= 0.306 Chirality : 0.039 0.165 3248 Planarity : 0.005 0.066 3510 Dihedral : 4.714 45.855 2841 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.51 % Allowed : 20.16 % Favored : 77.33 % 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: 0.63 (0.17), residues: 2687 helix: 1.60 (0.13), residues: 1850 sheet: -4.12 (0.80), residues: 30 loop : -2.33 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.015 0.001 TYR A 285 PHE 0.023 0.001 PHE D 532 TRP 0.065 0.002 TRP D 444 HIS 0.004 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (19662) covalent geometry : angle 0.60640 / 0.31 (26928) hydrogen bonds : bond 0.03397 / 2.37 ( 1245) hydrogen bonds : angle 4.01862 / 2.91 ( 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 195 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: F 113 ILE cc_start: 0.8871 (mm) cc_final: 0.8662 (mt) REVERT: F 188 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6779 (tm-30) REVERT: D 112 ARG cc_start: 0.6499 (mtm-85) cc_final: 0.5076 (tpp-160) REVERT: B 421 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7898 (mm) REVERT: C 89 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8070 (mtm180) REVERT: C 188 GLU cc_start: 0.7537 (tp30) cc_final: 0.7038 (tp30) REVERT: A 490 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8100 (mt) outliers start: 43 outliers final: 28 residues processed: 188 average time/residue: 0.1203 time to fit residues: 37.1291 Evaluate side-chains 176 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 449 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 58 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 96 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 449 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: 0.6980 chunk 186 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 151 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 257 optimal weight: 0.7980 chunk 169 optimal weight: 0.0030 chunk 67 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.161388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.121650 restraints weight = 92923.317| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 5.74 r_work: 0.3692 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1924 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= 0.119 Angle : 0.591 11.300 26928 Z= 0.297 Chirality : 0.039 0.163 3248 Planarity : 0.005 0.068 3510 Dihedral : 4.597 45.978 2841 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.01 % Allowed : 21.11 % 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: 0.71 (0.17), residues: 2687 helix: 1.66 (0.13), residues: 1852 sheet: -4.13 (0.81), residues: 30 loop : -2.27 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 492 TYR 0.015 0.001 TYR A 285 PHE 0.021 0.001 PHE A 532 TRP 0.060 0.001 TRP D 444 HIS 0.007 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (19662) covalent geometry : angle 0.59064 / 0.30 (26928) hydrogen bonds : bond 0.03228 / 2.26 ( 1245) hydrogen bonds : angle 3.93337 / 2.86 ( 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 188 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: F 188 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6759 (tm-30) REVERT: D 112 ARG cc_start: 0.6515 (mtm-85) cc_final: 0.5077 (tpp-160) REVERT: D 490 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 421 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7718 (mm) REVERT: C 89 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8044 (mtm180) REVERT: C 188 GLU cc_start: 0.7597 (tp30) cc_final: 0.7280 (tp30) REVERT: A 112 ARG cc_start: 0.6336 (mtt90) cc_final: 0.5104 (tpp-160) REVERT: A 490 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8207 (mt) outliers start: 34 outliers final: 26 residues processed: 185 average time/residue: 0.1315 time to fit residues: 39.5440 Evaluate side-chains 179 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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 449 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 58 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 89 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 264 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 97 optimal weight: 0.0270 chunk 180 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 81 optimal weight: 20.0000 chunk 173 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 497 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 = 0.4483 r_free = 0.4483 target = 0.161218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.121215 restraints weight = 98960.970| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 5.94 r_work: 0.3665 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19662 Z= 0.123 Angle : 0.606 11.333 26928 Z= 0.302 Chirality : 0.039 0.165 3248 Planarity : 0.005 0.068 3510 Dihedral : 4.545 46.378 2841 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.01 % Allowed : 21.16 % Favored : 76.83 % 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: 0.70 (0.17), residues: 2687 helix: 1.65 (0.13), residues: 1852 sheet: -4.07 (0.82), residues: 30 loop : -2.27 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 49 TYR 0.015 0.001 TYR A 285 PHE 0.021 0.001 PHE A 532 TRP 0.090 0.002 TRP D 444 HIS 0.004 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (19662) covalent geometry : angle 0.60628 / 0.30 (26928) hydrogen bonds : bond 0.03245 / 2.28 ( 1245) hydrogen bonds : angle 3.90966 / 2.84 ( 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 186 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: F 188 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6808 (tm-30) REVERT: D 112 ARG cc_start: 0.6473 (mtm-85) cc_final: 0.5036 (tpp-160) REVERT: D 475 HIS cc_start: 0.7314 (t-170) cc_final: 0.7101 (t-170) REVERT: B 421 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7806 (mm) REVERT: C 89 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8065 (mtm180) REVERT: C 188 GLU cc_start: 0.7634 (tp30) cc_final: 0.7299 (tp30) REVERT: A 112 ARG cc_start: 0.6326 (mtt90) cc_final: 0.5105 (tpp-160) REVERT: A 490 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8145 (mt) outliers start: 34 outliers final: 28 residues processed: 184 average time/residue: 0.1361 time to fit residues: 40.5558 Evaluate side-chains 179 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 50 CYS 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 449 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 58 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 89 ARG 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 398 LEU Chi-restraints excluded: chain A residue 449 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: 10.0000 chunk 10 optimal weight: 30.0000 chunk 82 optimal weight: 0.0170 chunk 110 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 211 optimal weight: 0.1980 chunk 99 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 overall best weight: 2.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.154798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.116704 restraints weight = 75891.045| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 4.69 r_work: 0.3556 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 19662 Z= 0.269 Angle : 0.733 11.610 26928 Z= 0.376 Chirality : 0.046 0.284 3248 Planarity : 0.005 0.068 3510 Dihedral : 5.061 42.805 2841 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.90 % Allowed : 21.27 % Favored : 76.83 % 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: 0.25 (0.17), residues: 2687 helix: 1.35 (0.13), residues: 1852 sheet: -4.47 (0.74), residues: 30 loop : -2.53 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 49 TYR 0.025 0.002 TYR A 285 PHE 0.028 0.003 PHE D 532 TRP 0.088 0.003 TRP D 444 HIS 0.012 0.002 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (19662) covalent geometry : angle 0.73280 / 0.38 (26928) hydrogen bonds : bond 0.04273 / 2.96 ( 1245) hydrogen bonds : angle 4.29148 / 3.11 ( 3699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5841.66 seconds wall clock time: 100 minutes 24.84 seconds (6024.84 seconds total)