Starting phenix.real_space_refine on Fri Jul 3 14:25:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ctf_30463/07_2026/7ctf_30463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ctf_30463/07_2026/7ctf_30463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ctf_30463/07_2026/7ctf_30463.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ctf_30463/07_2026/7ctf_30463.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ctf_30463/07_2026/7ctf_30463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ctf_30463/07_2026/7ctf_30463.map" model { file = "/net/cci-nas-00/data/ceres_data/7ctf_30463/07_2026/7ctf_30463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ctf_30463/07_2026/7ctf_30463.cif" } resolution = 4.8 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= 0.010 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 P 6 5.49 5 S 70 5.16 5 C 9314 2.51 5 N 2447 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 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: 14504 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 805 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "B" Number of atoms: 2460 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 302, 2460 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4828 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 567} Chain breaks: 7 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 3 Chain: "E" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3044 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 18, 'TRANS': 354} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.19 Number of scatterers: 14504 At special positions: 0 Unit cell: (119.318, 122.633, 150.805, 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) S 70 16.00 P 6 15.00 O 2667 8.00 N 2447 7.00 C 9314 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: 0.85 Conformation dependent library (CDL) restraints added in 564.8 milliseconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3454 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 11 sheets defined 62.2% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 761 through 769 removed outlier: 4.313A pdb=" N THR A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.625A pdb=" N ILE A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 Processing helix chain 'A' and resid 850 through 860 Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.250A pdb=" N LEU B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 removed outlier: 4.063A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.720A pdb=" N TRP B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 347 through 358 removed outlier: 3.632A pdb=" N VAL B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 383 removed outlier: 4.093A pdb=" N PHE B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 414 removed outlier: 3.830A pdb=" N GLN B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 removed outlier: 4.037A pdb=" N MET B 432 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 454 through 461 Processing helix chain 'B' and resid 473 through 483 removed outlier: 4.139A pdb=" N LEU B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 501 Processing helix chain 'B' and resid 512 through 522 Processing helix chain 'B' and resid 528 through 540 Processing helix chain 'B' and resid 566 through 573 removed outlier: 4.666A pdb=" N LEU B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 66 removed outlier: 3.689A pdb=" N ARG C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 83 removed outlier: 3.914A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.797A pdb=" N THR C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 163 removed outlier: 3.961A pdb=" N ILE C 162 " --> pdb=" O CYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 4.034A pdb=" N LEU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.682A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 264 through 270 Processing helix chain 'C' and resid 281 through 293 removed outlier: 4.376A pdb=" N THR C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.869A pdb=" N GLN C 339 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 removed outlier: 4.484A pdb=" N ARG C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 369 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 380 through 388 removed outlier: 4.635A pdb=" N ALA C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 425 removed outlier: 3.529A pdb=" N LEU C 394 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL C 415 " --> pdb=" O ASN C 411 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 442 removed outlier: 3.649A pdb=" N LEU C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 460 removed outlier: 3.503A pdb=" N ALA C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 482 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.690A pdb=" N HIS C 486 " --> pdb=" O TYR C 482 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 487 " --> pdb=" O CYS C 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 487' Processing helix chain 'C' and resid 492 through 501 Processing helix chain 'C' and resid 549 through 566 Processing helix chain 'C' and resid 569 through 574 Processing helix chain 'C' and resid 584 through 593 removed outlier: 4.207A pdb=" N GLU C 590 " --> pdb=" O HIS C 586 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 606 removed outlier: 3.626A pdb=" N HIS C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 Processing helix chain 'C' and resid 645 through 663 removed outlier: 3.774A pdb=" N TRP C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 691 removed outlier: 3.779A pdb=" N GLU C 687 " --> pdb=" O ARG C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 30 removed outlier: 3.839A pdb=" N GLU D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 57 removed outlier: 4.140A pdb=" N GLU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU D 50 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 removed outlier: 3.821A pdb=" N ILE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 119 through 123 removed outlier: 4.199A pdb=" N ASN D 122 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 160 through 165 removed outlier: 3.512A pdb=" N PHE D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 183 removed outlier: 4.491A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 202 Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.834A pdb=" N LYS D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 259 Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.517A pdb=" N ILE D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 removed outlier: 3.807A pdb=" N ALA D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 309 removed outlier: 3.737A pdb=" N CYS D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 removed outlier: 3.706A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.931A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 380 removed outlier: 3.652A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 376 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.792A pdb=" N ILE D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN D 416 " --> pdb=" O MET D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'E' and resid 11 through 23 removed outlier: 3.532A pdb=" N VAL E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY E 23 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.731A pdb=" N THR E 53 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.604A pdb=" N ILE E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 removed outlier: 3.764A pdb=" N LYS E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 removed outlier: 4.203A pdb=" N ASP E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 143 removed outlier: 3.720A pdb=" N ARG E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 161 through 166 removed outlier: 3.630A pdb=" N PHE E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 removed outlier: 3.501A pdb=" N LEU E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.676A pdb=" N GLY E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 244 Proline residue: E 234 - end of helix Proline residue: E 239 - end of helix Processing helix chain 'E' and resid 250 through 268 Proline residue: E 259 - end of helix removed outlier: 3.995A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 4.331A pdb=" N ASN E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 removed outlier: 4.356A pdb=" N PHE E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 328' Processing helix chain 'E' and resid 358 through 370 removed outlier: 3.567A pdb=" N LEU E 362 " --> pdb=" O PRO E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.783A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 422 Processing helix chain 'E' and resid 427 through 432 removed outlier: 3.675A pdb=" N TYR E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 832 through 833 Processing sheet with id=AA2, first strand: chain 'B' and resid 421 through 424 removed outlier: 7.045A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA4, first strand: chain 'B' and resid 546 through 549 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'C' and resid 105 through 106 removed outlier: 5.938A pdb=" N LEU C 105 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 695 through 696 removed outlier: 3.837A pdb=" N LYS C 695 " --> pdb=" O ALA C 705 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 705 " --> pdb=" O LYS C 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 66 removed outlier: 8.368A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 155 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.461A pdb=" N VAL E 59 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP E 125 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL E 61 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE E 33 " --> pdb=" O PHE E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 393 through 395 688 hydrogen bonds defined for protein. 2040 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: 1.84 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4527 1.34 - 1.46: 3121 1.46 - 1.58: 7040 1.58 - 1.70: 12 1.70 - 1.81: 104 Bond restraints: 14804 Sorted by residual: bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.30e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.87e+01 bond pdb=" C PRO C 570 " pdb=" N PRO C 571 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.30e-02 5.92e+03 3.22e+01 ... (remaining 14799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 19788 4.75 - 9.51: 218 9.51 - 14.26: 25 14.26 - 19.02: 3 19.02 - 23.77: 4 Bond angle restraints: 20038 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 116.10 23.77 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 117.13 19.70 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 120.20 16.63 1.00e+00 1.00e+00 2.76e+02 angle pdb=" C5 ATP E 901 " pdb=" C4 ATP E 901 " pdb=" N3 ATP E 901 " ideal model delta sigma weight residual 126.80 117.28 9.52 1.00e+00 1.00e+00 9.06e+01 ... (remaining 20033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7460 17.71 - 35.42: 1075 35.42 - 53.13: 311 53.13 - 70.83: 77 70.83 - 88.54: 16 Dihedral angle restraints: 8939 sinusoidal: 3669 harmonic: 5270 Sorted by residual: dihedral pdb=" CA ASP E 400 " pdb=" C ASP E 400 " pdb=" N GLN E 401 " pdb=" CA GLN E 401 " ideal model delta harmonic sigma weight residual 180.00 132.64 47.36 0 5.00e+00 4.00e-02 8.97e+01 dihedral pdb=" CA PRO C 628 " pdb=" C PRO C 628 " pdb=" N ASP C 629 " pdb=" CA ASP C 629 " ideal model delta harmonic sigma weight residual 180.00 136.83 43.17 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" CA GLN D 400 " pdb=" C GLN D 400 " pdb=" N LEU D 401 " pdb=" CA LEU D 401 " ideal model delta harmonic sigma weight residual 180.00 137.65 42.35 0 5.00e+00 4.00e-02 7.17e+01 ... (remaining 8936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1733 0.068 - 0.137: 474 0.137 - 0.205: 76 0.205 - 0.273: 10 0.273 - 0.342: 2 Chirality restraints: 2295 Sorted by residual: chirality pdb=" CG LEU B 570 " pdb=" CB LEU B 570 " pdb=" CD1 LEU B 570 " pdb=" CD2 LEU B 570 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA HIS E 195 " pdb=" N HIS E 195 " pdb=" C HIS E 195 " pdb=" CB HIS E 195 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE C 447 " pdb=" CA ILE C 447 " pdb=" CG1 ILE C 447 " pdb=" CG2 ILE C 447 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2292 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 400 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ASP E 400 " 0.063 2.00e-02 2.50e+03 pdb=" O ASP E 400 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN E 401 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 609 " 0.039 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR C 609 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 609 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 609 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 609 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 609 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 609 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 609 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 258 " 0.058 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO E 259 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO E 259 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 259 " 0.048 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3796 2.79 - 3.32: 13122 3.32 - 3.85: 24468 3.85 - 4.37: 26522 4.37 - 4.90: 44966 Nonbonded interactions: 112874 Sorted by model distance: nonbonded pdb=" O ALA C 654 " pdb=" OG1 THR C 658 " model vdw 2.264 3.040 nonbonded pdb=" O LYS C 202 " pdb=" OG1 THR C 206 " model vdw 2.287 3.040 nonbonded pdb=" O GLN C 339 " pdb=" OG SER C 342 " model vdw 2.299 3.040 nonbonded pdb=" O HIS C 284 " pdb=" OG1 THR C 287 " model vdw 2.301 3.040 nonbonded pdb=" O PHE C 118 " pdb=" OG1 THR C 122 " model vdw 2.307 3.040 ... (remaining 112869 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.190 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.009 0.090 14804 Z= 0.457 Angle : 1.363 23.770 20038 Z= 0.788 Chirality : 0.063 0.342 2295 Planarity : 0.009 0.086 2525 Dihedral : 18.699 88.542 5485 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 8.84 % Allowed : 17.50 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.62 % Twisted General : 0.95 % 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: -4.50 (0.15), residues: 1733 helix: -2.98 (0.11), residues: 945 sheet: -2.85 (0.35), residues: 155 loop : -2.69 (0.21), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 706 TYR 0.058 0.004 TYR C 609 PHE 0.055 0.005 PHE C 559 TRP 0.044 0.004 TRP E 162 HIS 0.010 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00872 / 0.46 (14804) covalent geometry : angle 1.36260 / 0.79 (20038) hydrogen bonds : bond 0.16089 / 10.98 ( 688) hydrogen bonds : angle 7.99072 / 5.60 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 684 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 THR cc_start: 0.8841 (p) cc_final: 0.8098 (t) REVERT: A 797 GLN cc_start: 0.9455 (mt0) cc_final: 0.9038 (mt0) REVERT: A 798 ILE cc_start: 0.9663 (pt) cc_final: 0.9365 (mp) REVERT: A 799 TYR cc_start: 0.9331 (t80) cc_final: 0.8855 (t80) REVERT: A 801 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8926 (mm110) REVERT: A 802 HIS cc_start: 0.8945 (t-90) cc_final: 0.8626 (t70) REVERT: A 811 LEU cc_start: 0.8878 (mt) cc_final: 0.8228 (mt) REVERT: A 816 MET cc_start: 0.9129 (ptt) cc_final: 0.8589 (pmm) REVERT: A 819 THR cc_start: 0.8959 (m) cc_final: 0.8155 (p) REVERT: A 834 VAL cc_start: 0.7992 (m) cc_final: 0.7592 (p) REVERT: A 838 ARG cc_start: 0.6516 (ttm-80) cc_final: 0.6298 (mtp-110) REVERT: A 847 LEU cc_start: 0.8727 (tp) cc_final: 0.8314 (tp) REVERT: B 302 MET cc_start: 0.9180 (tmm) cc_final: 0.8317 (tmm) REVERT: B 303 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8342 (tp) REVERT: B 305 LEU cc_start: 0.9194 (tp) cc_final: 0.8777 (pp) REVERT: B 324 GLU cc_start: 0.8583 (tp30) cc_final: 0.8215 (tp30) REVERT: B 327 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8474 (ttp80) REVERT: B 330 MET cc_start: 0.7848 (mtm) cc_final: 0.7513 (mmm) REVERT: B 331 LEU cc_start: 0.8867 (mp) cc_final: 0.8543 (mp) REVERT: B 335 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8667 (tp) REVERT: B 376 ILE cc_start: 0.9284 (tp) cc_final: 0.9017 (tt) REVERT: B 524 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.5939 (t80) REVERT: B 525 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7405 (mt) REVERT: B 536 LEU cc_start: 0.8858 (mt) cc_final: 0.8565 (tp) REVERT: C 47 TYR cc_start: 0.9124 (t80) cc_final: 0.8757 (t80) REVERT: C 66 ASN cc_start: 0.9344 (m-40) cc_final: 0.7818 (p0) REVERT: C 70 PHE cc_start: 0.9217 (p90) cc_final: 0.8934 (p90) REVERT: C 80 SER cc_start: 0.9468 (OUTLIER) cc_final: 0.8985 (p) REVERT: C 107 LEU cc_start: 0.9341 (mt) cc_final: 0.8902 (mt) REVERT: C 148 LEU cc_start: 0.9230 (tp) cc_final: 0.8817 (tt) REVERT: C 157 ASP cc_start: 0.8868 (m-30) cc_final: 0.8606 (p0) REVERT: C 162 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8190 (tp) REVERT: C 211 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: C 229 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8659 (p) REVERT: C 248 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8859 (pp) REVERT: C 285 LEU cc_start: 0.9413 (tp) cc_final: 0.8818 (tt) REVERT: C 314 PHE cc_start: 0.8789 (t80) cc_final: 0.8441 (t80) REVERT: C 315 LEU cc_start: 0.9584 (tp) cc_final: 0.9373 (tt) REVERT: C 317 HIS cc_start: 0.7928 (m90) cc_final: 0.6987 (m170) REVERT: C 318 ASP cc_start: 0.8769 (t70) cc_final: 0.7981 (t70) REVERT: C 326 LYS cc_start: 0.9269 (ttpt) cc_final: 0.8965 (ttmt) REVERT: C 334 GLU cc_start: 0.8463 (tp30) cc_final: 0.7787 (tp30) REVERT: C 341 LEU cc_start: 0.7912 (mt) cc_final: 0.7605 (mt) REVERT: C 363 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8505 (t) REVERT: C 369 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.5759 (tt) REVERT: C 409 HIS cc_start: 0.9405 (m-70) cc_final: 0.9126 (m-70) REVERT: C 469 MET cc_start: 0.6965 (ttm) cc_final: 0.6676 (mtt) REVERT: C 604 LEU cc_start: 0.9672 (mt) cc_final: 0.9205 (mm) REVERT: C 634 TYR cc_start: 0.9041 (t80) cc_final: 0.8483 (t80) REVERT: C 635 LYS cc_start: 0.7832 (tttt) cc_final: 0.7456 (tptt) REVERT: C 657 VAL cc_start: 0.9617 (OUTLIER) cc_final: 0.9298 (m) REVERT: C 671 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: C 674 ASN cc_start: 0.8985 (t0) cc_final: 0.8188 (m-40) REVERT: C 693 PHE cc_start: 0.8643 (m-80) cc_final: 0.8367 (m-80) REVERT: D 24 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.7150 (tt) REVERT: D 28 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.6503 (m-10) REVERT: D 64 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7657 (mt) REVERT: D 81 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.8849 (mt) REVERT: D 84 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9366 (pp) REVERT: D 85 MET cc_start: 0.8545 (mmm) cc_final: 0.8270 (mmm) REVERT: D 97 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8473 (p) REVERT: D 107 ASP cc_start: 0.8215 (t0) cc_final: 0.7946 (t0) REVERT: D 164 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7596 (t80) REVERT: D 179 ILE cc_start: 0.9366 (mt) cc_final: 0.9132 (tt) REVERT: D 185 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8727 (m) REVERT: D 187 ILE cc_start: 0.8961 (mt) cc_final: 0.8682 (mt) REVERT: D 201 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8563 (tt) REVERT: D 226 TYR cc_start: 0.8798 (t80) cc_final: 0.8313 (t80) REVERT: D 284 MET cc_start: 0.9123 (tpt) cc_final: 0.8868 (tpp) REVERT: D 297 MET cc_start: 0.8415 (ptm) cc_final: 0.7185 (ptm) REVERT: D 326 ILE cc_start: 0.9477 (mt) cc_final: 0.9135 (mt) REVERT: D 348 MET cc_start: 0.8701 (tpt) cc_final: 0.8120 (tpt) REVERT: D 352 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8769 (mm-30) REVERT: D 377 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: D 380 GLN cc_start: 0.9023 (tt0) cc_final: 0.8670 (tm-30) REVERT: D 402 MET cc_start: 0.8415 (mtt) cc_final: 0.7634 (mtt) REVERT: E 10 CYS cc_start: 0.7540 (m) cc_final: 0.6927 (m) REVERT: E 19 GLN cc_start: 0.9271 (tt0) cc_final: 0.8963 (tm-30) REVERT: E 21 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9059 (mt) REVERT: E 27 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7046 (p90) REVERT: E 34 PHE cc_start: 0.9455 (t80) cc_final: 0.9000 (t80) REVERT: E 35 ILE cc_start: 0.9326 (mt) cc_final: 0.8896 (mm) REVERT: E 49 THR cc_start: 0.8772 (p) cc_final: 0.8487 (p) REVERT: E 76 ILE cc_start: 0.9667 (mt) cc_final: 0.9415 (mt) REVERT: E 105 LEU cc_start: 0.8748 (mt) cc_final: 0.7824 (mt) REVERT: E 126 LYS cc_start: 0.8764 (mtpp) cc_final: 0.7905 (tttm) REVERT: E 129 TYR cc_start: 0.8829 (m-10) cc_final: 0.7979 (m-10) REVERT: E 144 LEU cc_start: 0.9296 (tp) cc_final: 0.9006 (tt) REVERT: E 155 LEU cc_start: 0.9168 (tp) cc_final: 0.8936 (tp) REVERT: E 160 ILE cc_start: 0.9335 (tp) cc_final: 0.8591 (tt) REVERT: E 171 CYS cc_start: 0.7077 (t) cc_final: 0.6749 (t) REVERT: E 172 PHE cc_start: 0.8098 (t80) cc_final: 0.7797 (t80) REVERT: E 223 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8312 (mptt) REVERT: E 227 HIS cc_start: 0.9013 (t70) cc_final: 0.8651 (t-90) REVERT: E 253 LEU cc_start: 0.8725 (tp) cc_final: 0.8366 (mp) REVERT: E 257 ILE cc_start: 0.8418 (tp) cc_final: 0.8000 (tp) REVERT: E 307 LYS cc_start: 0.9537 (mttp) cc_final: 0.9265 (mttm) REVERT: E 314 TYR cc_start: 0.8082 (t80) cc_final: 0.7766 (t80) REVERT: E 380 ILE cc_start: 0.9065 (tp) cc_final: 0.8615 (tp) REVERT: E 401 GLN cc_start: 0.5416 (mm-40) cc_final: 0.4801 (mm-40) REVERT: E 409 CYS cc_start: 0.6693 (t) cc_final: 0.6424 (t) REVERT: E 431 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8372 (pp) outliers start: 144 outliers final: 24 residues processed: 763 average time/residue: 0.1052 time to fit residues: 117.1577 Evaluate side-chains 459 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 408 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 4.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS B 372 GLN B 428 ASN C 48 GLN C 58 ASN C 146 HIS ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN C 335 HIS C 347 ASN C 555 ASN C 605 ASN C 613 ASN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 HIS D 170 GLN D 252 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS D 288 ASN D 351 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN E 227 HIS E 266 GLN E 299 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054540 restraints weight = 66044.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.056425 restraints weight = 45114.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057618 restraints weight = 33946.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058813 restraints weight = 27474.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059633 restraints weight = 22968.777| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14804 Z= 0.162 Angle : 0.805 13.153 20038 Z= 0.416 Chirality : 0.046 0.231 2295 Planarity : 0.006 0.075 2525 Dihedral : 7.751 86.986 1902 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.31 % Allowed : 4.97 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.18 % 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: -2.70 (0.18), residues: 1733 helix: -1.19 (0.15), residues: 972 sheet: -2.50 (0.35), residues: 161 loop : -2.38 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 289 TYR 0.026 0.002 TYR C 567 PHE 0.037 0.003 PHE B 492 TRP 0.035 0.003 TRP C 649 HIS 0.008 0.001 HIS C 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14804) covalent geometry : angle 0.80517 / 0.42 (20038) hydrogen bonds : bond 0.05210 / 3.47 ( 688) hydrogen bonds : angle 5.70534 / 4.03 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 516 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9299 (t80) cc_final: 0.9060 (t80) REVERT: A 795 PHE cc_start: 0.8769 (t80) cc_final: 0.8410 (t80) REVERT: A 797 GLN cc_start: 0.9304 (mt0) cc_final: 0.9008 (pt0) REVERT: A 799 TYR cc_start: 0.9126 (t80) cc_final: 0.8742 (t80) REVERT: A 801 GLN cc_start: 0.9529 (mm-40) cc_final: 0.9031 (mm110) REVERT: A 816 MET cc_start: 0.9301 (ptt) cc_final: 0.9094 (pmm) REVERT: A 819 THR cc_start: 0.9203 (m) cc_final: 0.8580 (p) REVERT: A 825 HIS cc_start: 0.9430 (m90) cc_final: 0.9193 (m-70) REVERT: A 826 LEU cc_start: 0.9407 (mt) cc_final: 0.9030 (mt) REVERT: A 834 VAL cc_start: 0.9069 (m) cc_final: 0.8825 (p) REVERT: A 842 LEU cc_start: 0.9145 (mm) cc_final: 0.8925 (mm) REVERT: A 845 VAL cc_start: 0.9427 (t) cc_final: 0.9212 (p) REVERT: B 301 TRP cc_start: 0.9136 (m-10) cc_final: 0.8804 (m-10) REVERT: B 302 MET cc_start: 0.9441 (tmm) cc_final: 0.8778 (tmm) REVERT: B 303 LEU cc_start: 0.9550 (tt) cc_final: 0.9262 (tp) REVERT: B 324 GLU cc_start: 0.9012 (tp30) cc_final: 0.8278 (mt-10) REVERT: B 330 MET cc_start: 0.8081 (mtm) cc_final: 0.7879 (mmm) REVERT: B 348 VAL cc_start: 0.9476 (m) cc_final: 0.9257 (m) REVERT: B 388 LEU cc_start: 0.8975 (tp) cc_final: 0.8516 (mm) REVERT: B 394 ASN cc_start: 0.8835 (t0) cc_final: 0.8631 (t0) REVERT: B 403 GLU cc_start: 0.9310 (mp0) cc_final: 0.9082 (mp0) REVERT: B 426 HIS cc_start: 0.8970 (t-90) cc_final: 0.8397 (t70) REVERT: B 432 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8079 (ptm) REVERT: B 434 ASP cc_start: 0.8264 (p0) cc_final: 0.7713 (p0) REVERT: B 532 LEU cc_start: 0.8786 (tp) cc_final: 0.8426 (tp) REVERT: B 536 LEU cc_start: 0.9027 (mt) cc_final: 0.8756 (pp) REVERT: C 66 ASN cc_start: 0.9142 (m-40) cc_final: 0.8169 (p0) REVERT: C 70 PHE cc_start: 0.9393 (p90) cc_final: 0.8970 (p90) REVERT: C 73 LEU cc_start: 0.9743 (tt) cc_final: 0.9489 (tt) REVERT: C 147 PHE cc_start: 0.9419 (t80) cc_final: 0.9099 (t80) REVERT: C 148 LEU cc_start: 0.9295 (tp) cc_final: 0.8993 (tt) REVERT: C 222 MET cc_start: 0.8720 (tmm) cc_final: 0.8252 (tmm) REVERT: C 232 ASP cc_start: 0.9262 (m-30) cc_final: 0.9047 (m-30) REVERT: C 314 PHE cc_start: 0.9034 (t80) cc_final: 0.8583 (t80) REVERT: C 315 LEU cc_start: 0.9755 (tp) cc_final: 0.9553 (tt) REVERT: C 318 ASP cc_start: 0.8777 (t70) cc_final: 0.8296 (t70) REVERT: C 325 ILE cc_start: 0.9704 (mt) cc_final: 0.9471 (pt) REVERT: C 326 LYS cc_start: 0.9667 (ttpt) cc_final: 0.9357 (tttt) REVERT: C 334 GLU cc_start: 0.9396 (tp30) cc_final: 0.8387 (tp30) REVERT: C 410 MET cc_start: 0.9601 (mtm) cc_final: 0.9325 (mtt) REVERT: C 581 TYR cc_start: 0.8172 (m-10) cc_final: 0.7939 (m-10) REVERT: C 582 PHE cc_start: 0.7042 (t80) cc_final: 0.5497 (t80) REVERT: C 592 LEU cc_start: 0.9534 (tp) cc_final: 0.9334 (tp) REVERT: C 688 LEU cc_start: 0.9620 (mm) cc_final: 0.9385 (mm) REVERT: C 693 PHE cc_start: 0.9285 (m-80) cc_final: 0.9074 (m-80) REVERT: D 38 PHE cc_start: 0.6622 (t80) cc_final: 0.6186 (t80) REVERT: D 107 ASP cc_start: 0.8597 (t0) cc_final: 0.8100 (t0) REVERT: D 155 ILE cc_start: 0.9588 (mm) cc_final: 0.9252 (tp) REVERT: D 156 PHE cc_start: 0.9565 (m-10) cc_final: 0.9324 (m-10) REVERT: D 164 PHE cc_start: 0.9442 (m-80) cc_final: 0.8973 (m-80) REVERT: D 177 PHE cc_start: 0.9348 (m-10) cc_final: 0.9115 (m-10) REVERT: D 225 GLN cc_start: 0.9295 (mp10) cc_final: 0.8969 (mp10) REVERT: D 226 TYR cc_start: 0.9474 (t80) cc_final: 0.8823 (t80) REVERT: D 282 LEU cc_start: 0.9392 (tt) cc_final: 0.9121 (tp) REVERT: D 297 MET cc_start: 0.8621 (ptm) cc_final: 0.7582 (ptm) REVERT: D 298 THR cc_start: 0.9428 (p) cc_final: 0.9223 (t) REVERT: D 321 LEU cc_start: 0.8975 (mt) cc_final: 0.8586 (mt) REVERT: D 330 ILE cc_start: 0.9624 (mt) cc_final: 0.9327 (mt) REVERT: D 333 LYS cc_start: 0.9395 (tmmt) cc_final: 0.8865 (mtpt) REVERT: D 339 TYR cc_start: 0.7710 (t80) cc_final: 0.7003 (t80) REVERT: D 346 PHE cc_start: 0.9285 (t80) cc_final: 0.8467 (t80) REVERT: D 378 HIS cc_start: 0.9646 (t-90) cc_final: 0.9166 (t70) REVERT: D 379 LEU cc_start: 0.9447 (tp) cc_final: 0.8971 (mp) REVERT: D 380 GLN cc_start: 0.9283 (tt0) cc_final: 0.8888 (tp40) REVERT: D 401 LEU cc_start: 0.9073 (tp) cc_final: 0.8580 (tp) REVERT: D 406 LEU cc_start: 0.8725 (mt) cc_final: 0.8375 (mt) REVERT: D 412 MET cc_start: 0.9403 (mmm) cc_final: 0.9202 (mtt) REVERT: D 418 TYR cc_start: 0.7561 (t80) cc_final: 0.7231 (t80) REVERT: E 19 GLN cc_start: 0.9621 (tt0) cc_final: 0.9199 (tm-30) REVERT: E 21 LEU cc_start: 0.9397 (tt) cc_final: 0.9196 (mt) REVERT: E 34 PHE cc_start: 0.9463 (t80) cc_final: 0.9195 (t80) REVERT: E 64 VAL cc_start: 0.8772 (t) cc_final: 0.8290 (t) REVERT: E 107 LYS cc_start: 0.9422 (mttm) cc_final: 0.9216 (mmmt) REVERT: E 141 PHE cc_start: 0.9066 (m-80) cc_final: 0.8479 (m-80) REVERT: E 160 ILE cc_start: 0.9152 (tp) cc_final: 0.8641 (tt) REVERT: E 172 PHE cc_start: 0.8500 (t80) cc_final: 0.8033 (t80) REVERT: E 192 SER cc_start: 0.7473 (p) cc_final: 0.6580 (t) REVERT: E 208 ILE cc_start: 0.9627 (pt) cc_final: 0.9326 (pt) REVERT: E 223 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7817 (mptt) REVERT: E 236 TYR cc_start: 0.7920 (t80) cc_final: 0.7377 (t80) REVERT: E 383 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8300 (tm-30) REVERT: E 391 GLN cc_start: 0.8554 (mm110) cc_final: 0.8301 (mm110) REVERT: E 392 LEU cc_start: 0.9168 (mt) cc_final: 0.8189 (pp) REVERT: E 409 CYS cc_start: 0.7010 (t) cc_final: 0.6585 (t) outliers start: 5 outliers final: 1 residues processed: 520 average time/residue: 0.0945 time to fit residues: 74.0563 Evaluate side-chains 375 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 8 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN B 438 GLN C 58 ASN C 242 HIS C 322 GLN C 399 GLN C 406 HIS C 555 ASN ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN D 79 HIS D 233 GLN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.050947 restraints weight = 72471.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052578 restraints weight = 50003.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053862 restraints weight = 38209.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054806 restraints weight = 30735.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055553 restraints weight = 25999.749| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (25 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14804 Z= 0.216 Angle : 0.796 14.685 20038 Z= 0.410 Chirality : 0.046 0.201 2295 Planarity : 0.005 0.061 2525 Dihedral : 7.130 84.912 1902 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.12 % 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: -1.87 (0.19), residues: 1733 helix: -0.52 (0.15), residues: 961 sheet: -2.56 (0.38), residues: 141 loop : -1.88 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 368 TYR 0.023 0.002 TYR C 567 PHE 0.029 0.002 PHE C 559 TRP 0.022 0.002 TRP B 445 HIS 0.009 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.22 (14804) covalent geometry : angle 0.79621 / 0.41 (20038) hydrogen bonds : bond 0.04517 / 2.99 ( 688) hydrogen bonds : angle 5.52586 / 3.90 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 415 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9461 (t80) cc_final: 0.9219 (t80) REVERT: A 781 ILE cc_start: 0.9653 (mt) cc_final: 0.9438 (mt) REVERT: A 798 ILE cc_start: 0.9741 (pt) cc_final: 0.9204 (tt) REVERT: A 801 GLN cc_start: 0.9614 (mm-40) cc_final: 0.8405 (mm-40) REVERT: A 816 MET cc_start: 0.9483 (ptt) cc_final: 0.8919 (pmm) REVERT: A 825 HIS cc_start: 0.9506 (m90) cc_final: 0.9177 (m90) REVERT: A 826 LEU cc_start: 0.9435 (mt) cc_final: 0.9038 (mt) REVERT: A 834 VAL cc_start: 0.9150 (m) cc_final: 0.8935 (p) REVERT: A 844 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8566 (mmt-90) REVERT: A 845 VAL cc_start: 0.9244 (t) cc_final: 0.9008 (p) REVERT: B 301 TRP cc_start: 0.9124 (m-10) cc_final: 0.8886 (m-10) REVERT: B 303 LEU cc_start: 0.9544 (tt) cc_final: 0.9058 (tp) REVERT: B 330 MET cc_start: 0.8110 (mtm) cc_final: 0.7828 (mmm) REVERT: B 388 LEU cc_start: 0.9123 (tp) cc_final: 0.8544 (mm) REVERT: B 394 ASN cc_start: 0.9123 (t0) cc_final: 0.8866 (t0) REVERT: B 403 GLU cc_start: 0.9368 (mp0) cc_final: 0.8882 (mp0) REVERT: B 426 HIS cc_start: 0.9006 (t-90) cc_final: 0.8445 (t70) REVERT: B 432 MET cc_start: 0.8307 (ptt) cc_final: 0.8058 (ptm) REVERT: B 532 LEU cc_start: 0.8829 (tp) cc_final: 0.8525 (tp) REVERT: B 536 LEU cc_start: 0.9041 (mt) cc_final: 0.8771 (pp) REVERT: C 66 ASN cc_start: 0.9302 (m-40) cc_final: 0.8694 (m-40) REVERT: C 77 LEU cc_start: 0.9573 (mt) cc_final: 0.9193 (pp) REVERT: C 144 MET cc_start: 0.8760 (mmp) cc_final: 0.7389 (mmm) REVERT: C 148 LEU cc_start: 0.9213 (tp) cc_final: 0.8757 (tt) REVERT: C 232 ASP cc_start: 0.9183 (m-30) cc_final: 0.8787 (p0) REVERT: C 246 LEU cc_start: 0.9012 (mt) cc_final: 0.8711 (mt) REVERT: C 318 ASP cc_start: 0.8993 (t70) cc_final: 0.8571 (t70) REVERT: C 326 LYS cc_start: 0.9597 (ttpt) cc_final: 0.9015 (tttp) REVERT: C 330 LEU cc_start: 0.9693 (tp) cc_final: 0.9372 (tp) REVERT: C 333 LEU cc_start: 0.9647 (mt) cc_final: 0.9415 (mt) REVERT: C 334 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9049 (mt-10) REVERT: C 393 TYR cc_start: 0.9202 (m-80) cc_final: 0.8991 (m-80) REVERT: C 410 MET cc_start: 0.9670 (mtm) cc_final: 0.9366 (mtp) REVERT: C 419 LEU cc_start: 0.9793 (pp) cc_final: 0.9241 (pp) REVERT: C 582 PHE cc_start: 0.7179 (t80) cc_final: 0.6451 (t80) REVERT: C 592 LEU cc_start: 0.9644 (tp) cc_final: 0.9413 (pp) REVERT: C 688 LEU cc_start: 0.9615 (mm) cc_final: 0.9313 (mm) REVERT: D 38 PHE cc_start: 0.6845 (t80) cc_final: 0.6279 (t80) REVERT: D 75 MET cc_start: 0.9185 (ptm) cc_final: 0.8783 (ptm) REVERT: D 107 ASP cc_start: 0.8577 (t0) cc_final: 0.8159 (t0) REVERT: D 157 ILE cc_start: 0.9527 (mp) cc_final: 0.9248 (mp) REVERT: D 160 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 163 LEU cc_start: 0.9617 (tt) cc_final: 0.9247 (tt) REVERT: D 164 PHE cc_start: 0.9497 (m-80) cc_final: 0.9016 (m-80) REVERT: D 192 LEU cc_start: 0.9314 (mm) cc_final: 0.9096 (mm) REVERT: D 198 ILE cc_start: 0.9539 (tp) cc_final: 0.9226 (mm) REVERT: D 225 GLN cc_start: 0.9146 (mp10) cc_final: 0.8905 (mp10) REVERT: D 282 LEU cc_start: 0.9604 (tt) cc_final: 0.9289 (tp) REVERT: D 297 MET cc_start: 0.8896 (ptm) cc_final: 0.8046 (ptm) REVERT: D 302 LEU cc_start: 0.9683 (mm) cc_final: 0.9460 (mm) REVERT: D 312 ASP cc_start: 0.8532 (p0) cc_final: 0.8240 (p0) REVERT: D 321 LEU cc_start: 0.9060 (mt) cc_final: 0.8757 (mt) REVERT: D 339 TYR cc_start: 0.7912 (t80) cc_final: 0.7238 (t80) REVERT: D 348 MET cc_start: 0.9336 (mmm) cc_final: 0.8296 (mmm) REVERT: D 378 HIS cc_start: 0.9642 (t-90) cc_final: 0.9436 (t70) REVERT: D 401 LEU cc_start: 0.8850 (tp) cc_final: 0.8573 (tp) REVERT: D 406 LEU cc_start: 0.9099 (mt) cc_final: 0.8802 (mt) REVERT: D 418 TYR cc_start: 0.7768 (t80) cc_final: 0.7553 (t80) REVERT: E 19 GLN cc_start: 0.9676 (tt0) cc_final: 0.9138 (tm-30) REVERT: E 34 PHE cc_start: 0.9416 (t80) cc_final: 0.9127 (t80) REVERT: E 160 ILE cc_start: 0.9095 (tp) cc_final: 0.8822 (mt) REVERT: E 172 PHE cc_start: 0.8936 (t80) cc_final: 0.8609 (t80) REVERT: E 204 TYR cc_start: 0.8958 (t80) cc_final: 0.8656 (t80) REVERT: E 223 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8125 (mptt) REVERT: E 236 TYR cc_start: 0.8262 (t80) cc_final: 0.7903 (t80) REVERT: E 318 TYR cc_start: 0.8840 (m-10) cc_final: 0.8603 (m-10) REVERT: E 351 LEU cc_start: 0.9107 (mt) cc_final: 0.8351 (pp) REVERT: E 409 CYS cc_start: 0.7638 (t) cc_final: 0.7154 (t) outliers start: 2 outliers final: 1 residues processed: 417 average time/residue: 0.0953 time to fit residues: 60.1706 Evaluate side-chains 322 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 172 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 32 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 797 GLN A 802 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN B 393 HIS B 435 HIS C 58 ASN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS E 227 HIS E 266 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.070668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053339 restraints weight = 69174.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055158 restraints weight = 47561.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056519 restraints weight = 35744.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057538 restraints weight = 28590.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058353 restraints weight = 23971.284| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14804 Z= 0.128 Angle : 0.727 16.268 20038 Z= 0.364 Chirality : 0.045 0.228 2295 Planarity : 0.004 0.066 2525 Dihedral : 6.733 89.204 1902 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.58 (0.19), residues: 1733 helix: -0.28 (0.16), residues: 990 sheet: -2.01 (0.42), residues: 127 loop : -1.96 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 104 TYR 0.022 0.002 TYR C 567 PHE 0.028 0.002 PHE B 492 TRP 0.014 0.002 TRP B 443 HIS 0.009 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (14804) covalent geometry : angle 0.72746 / 0.36 (20038) hydrogen bonds : bond 0.03961 / 2.64 ( 688) hydrogen bonds : angle 5.14620 / 3.65 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 GLN cc_start: 0.9677 (mp10) cc_final: 0.9463 (pt0) REVERT: A 798 ILE cc_start: 0.9543 (pt) cc_final: 0.9282 (mp) REVERT: A 799 TYR cc_start: 0.9328 (t80) cc_final: 0.8909 (t80) REVERT: A 801 GLN cc_start: 0.9495 (mm-40) cc_final: 0.9182 (mp10) REVERT: A 816 MET cc_start: 0.9647 (ptt) cc_final: 0.8839 (pmm) REVERT: A 825 HIS cc_start: 0.9560 (m90) cc_final: 0.9165 (m90) REVERT: A 826 LEU cc_start: 0.9486 (mt) cc_final: 0.9180 (mt) REVERT: B 301 TRP cc_start: 0.8927 (m-10) cc_final: 0.8706 (m-10) REVERT: B 302 MET cc_start: 0.9130 (ppp) cc_final: 0.8927 (ppp) REVERT: B 330 MET cc_start: 0.8126 (mtm) cc_final: 0.7820 (mmm) REVERT: B 388 LEU cc_start: 0.9035 (tp) cc_final: 0.8575 (mm) REVERT: B 394 ASN cc_start: 0.9007 (t0) cc_final: 0.8794 (p0) REVERT: B 426 HIS cc_start: 0.8916 (t-90) cc_final: 0.8450 (t70) REVERT: B 432 MET cc_start: 0.8439 (ptt) cc_final: 0.8068 (ptm) REVERT: B 517 TYR cc_start: 0.7143 (t80) cc_final: 0.6860 (t80) REVERT: B 532 LEU cc_start: 0.8817 (tp) cc_final: 0.8344 (tt) REVERT: C 54 MET cc_start: 0.9504 (mmp) cc_final: 0.9297 (mmm) REVERT: C 66 ASN cc_start: 0.9349 (m-40) cc_final: 0.8575 (p0) REVERT: C 77 LEU cc_start: 0.9529 (mt) cc_final: 0.9154 (pp) REVERT: C 144 MET cc_start: 0.8748 (mmp) cc_final: 0.8543 (mmm) REVERT: C 148 LEU cc_start: 0.9124 (tp) cc_final: 0.8589 (tt) REVERT: C 246 LEU cc_start: 0.9032 (mt) cc_final: 0.8757 (mt) REVERT: C 318 ASP cc_start: 0.8927 (t70) cc_final: 0.8721 (t70) REVERT: C 326 LYS cc_start: 0.9583 (ttpt) cc_final: 0.9030 (tttp) REVERT: C 330 LEU cc_start: 0.9681 (tp) cc_final: 0.9173 (tp) REVERT: C 333 LEU cc_start: 0.9672 (mt) cc_final: 0.9350 (mt) REVERT: C 410 MET cc_start: 0.9657 (mtm) cc_final: 0.9362 (mtp) REVERT: C 582 PHE cc_start: 0.7138 (t80) cc_final: 0.6482 (t80) REVERT: C 590 GLU cc_start: 0.9329 (mp0) cc_final: 0.8879 (pm20) REVERT: C 592 LEU cc_start: 0.9669 (tp) cc_final: 0.9454 (tp) REVERT: C 634 TYR cc_start: 0.9492 (t80) cc_final: 0.9208 (t80) REVERT: C 688 LEU cc_start: 0.9554 (mm) cc_final: 0.9330 (mm) REVERT: C 690 LEU cc_start: 0.9694 (tt) cc_final: 0.9447 (tt) REVERT: D 28 PHE cc_start: 0.8333 (m-80) cc_final: 0.7874 (m-80) REVERT: D 38 PHE cc_start: 0.6613 (t80) cc_final: 0.6023 (t80) REVERT: D 75 MET cc_start: 0.9098 (ptm) cc_final: 0.8747 (ptm) REVERT: D 107 ASP cc_start: 0.8589 (t0) cc_final: 0.8153 (t0) REVERT: D 164 PHE cc_start: 0.9495 (m-80) cc_final: 0.9152 (m-80) REVERT: D 177 PHE cc_start: 0.9157 (m-10) cc_final: 0.8905 (m-10) REVERT: D 198 ILE cc_start: 0.9548 (tp) cc_final: 0.9315 (mm) REVERT: D 225 GLN cc_start: 0.9148 (mp10) cc_final: 0.8846 (mp10) REVERT: D 249 TRP cc_start: 0.8602 (t-100) cc_final: 0.8354 (t-100) REVERT: D 281 MET cc_start: 0.9294 (ppp) cc_final: 0.9069 (ppp) REVERT: D 297 MET cc_start: 0.8335 (ptm) cc_final: 0.7120 (ttm) REVERT: D 311 MET cc_start: 0.5995 (mpp) cc_final: 0.5191 (mpp) REVERT: D 312 ASP cc_start: 0.8437 (p0) cc_final: 0.8111 (p0) REVERT: D 321 LEU cc_start: 0.8958 (mt) cc_final: 0.8689 (mt) REVERT: D 339 TYR cc_start: 0.7852 (t80) cc_final: 0.7149 (t80) REVERT: D 348 MET cc_start: 0.9306 (mmm) cc_final: 0.8291 (mmm) REVERT: D 418 TYR cc_start: 0.7487 (t80) cc_final: 0.7285 (t80) REVERT: E 19 GLN cc_start: 0.9676 (tt0) cc_final: 0.9124 (tm-30) REVERT: E 34 PHE cc_start: 0.9407 (t80) cc_final: 0.9034 (t80) REVERT: E 76 ILE cc_start: 0.9538 (mt) cc_final: 0.9232 (mt) REVERT: E 105 LEU cc_start: 0.8338 (mt) cc_final: 0.8129 (mt) REVERT: E 129 TYR cc_start: 0.8705 (m-10) cc_final: 0.8312 (m-10) REVERT: E 132 ASP cc_start: 0.9644 (m-30) cc_final: 0.9382 (p0) REVERT: E 133 MET cc_start: 0.7468 (mmm) cc_final: 0.7001 (mmm) REVERT: E 141 PHE cc_start: 0.9010 (m-80) cc_final: 0.8732 (m-80) REVERT: E 223 LYS cc_start: 0.8583 (mtpt) cc_final: 0.7998 (mptt) REVERT: E 236 TYR cc_start: 0.8271 (t80) cc_final: 0.7924 (t80) REVERT: E 314 TYR cc_start: 0.8910 (t80) cc_final: 0.8222 (t80) REVERT: E 351 LEU cc_start: 0.8952 (mt) cc_final: 0.8231 (pp) REVERT: E 379 ASN cc_start: 0.9442 (t0) cc_final: 0.8991 (t0) REVERT: E 416 ILE cc_start: 0.9194 (mm) cc_final: 0.8963 (mm) outliers start: 1 outliers final: 1 residues processed: 414 average time/residue: 0.0870 time to fit residues: 55.3646 Evaluate side-chains 337 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN B 411 GLN C 409 HIS C 558 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.070345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.053627 restraints weight = 70273.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055345 restraints weight = 49094.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056609 restraints weight = 37311.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057593 restraints weight = 30163.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058281 restraints weight = 25549.503| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14804 Z= 0.131 Angle : 0.721 16.499 20038 Z= 0.359 Chirality : 0.044 0.225 2295 Planarity : 0.005 0.081 2525 Dihedral : 6.469 85.693 1902 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.43 (0.20), residues: 1733 helix: -0.15 (0.16), residues: 992 sheet: -1.80 (0.43), residues: 129 loop : -1.97 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 104 TYR 0.019 0.001 TYR C 567 PHE 0.027 0.002 PHE B 492 TRP 0.031 0.002 TRP B 445 HIS 0.005 0.001 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14804) covalent geometry : angle 0.72058 / 0.36 (20038) hydrogen bonds : bond 0.03762 / 2.50 ( 688) hydrogen bonds : angle 5.03100 / 3.57 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9304 (t80) cc_final: 0.9076 (t80) REVERT: A 799 TYR cc_start: 0.9377 (t80) cc_final: 0.9072 (t80) REVERT: A 816 MET cc_start: 0.9480 (ptt) cc_final: 0.8864 (pmm) REVERT: A 820 MET cc_start: 0.9572 (mmp) cc_final: 0.9272 (mmm) REVERT: A 825 HIS cc_start: 0.9566 (m90) cc_final: 0.9169 (m90) REVERT: A 826 LEU cc_start: 0.9446 (mt) cc_final: 0.9109 (mt) REVERT: B 301 TRP cc_start: 0.8955 (m-10) cc_final: 0.8692 (m-10) REVERT: B 302 MET cc_start: 0.9178 (ppp) cc_final: 0.8964 (ppp) REVERT: B 303 LEU cc_start: 0.9058 (tp) cc_final: 0.8839 (tp) REVERT: B 330 MET cc_start: 0.8206 (mtm) cc_final: 0.7875 (mmm) REVERT: B 388 LEU cc_start: 0.9069 (tp) cc_final: 0.8617 (mm) REVERT: B 426 HIS cc_start: 0.8810 (t-90) cc_final: 0.8265 (t70) REVERT: B 432 MET cc_start: 0.8496 (ptt) cc_final: 0.8073 (ptm) REVERT: B 532 LEU cc_start: 0.8793 (tp) cc_final: 0.8516 (tt) REVERT: C 54 MET cc_start: 0.9602 (mmp) cc_final: 0.9377 (mmm) REVERT: C 66 ASN cc_start: 0.9405 (m-40) cc_final: 0.8505 (p0) REVERT: C 77 LEU cc_start: 0.9497 (mt) cc_final: 0.9152 (pp) REVERT: C 144 MET cc_start: 0.8909 (mmp) cc_final: 0.8671 (mmm) REVERT: C 148 LEU cc_start: 0.9103 (tp) cc_final: 0.8569 (tt) REVERT: C 222 MET cc_start: 0.8273 (tmm) cc_final: 0.7953 (tmm) REVERT: C 246 LEU cc_start: 0.9023 (mt) cc_final: 0.8781 (mt) REVERT: C 326 LYS cc_start: 0.9589 (ttpt) cc_final: 0.9102 (tttp) REVERT: C 330 LEU cc_start: 0.9692 (tp) cc_final: 0.9120 (tp) REVERT: C 333 LEU cc_start: 0.9641 (mt) cc_final: 0.9347 (mt) REVERT: C 334 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9176 (mm-30) REVERT: C 393 TYR cc_start: 0.9159 (m-80) cc_final: 0.8898 (m-80) REVERT: C 410 MET cc_start: 0.9641 (mtm) cc_final: 0.9322 (mtp) REVERT: C 567 TYR cc_start: 0.8791 (t80) cc_final: 0.8524 (t80) REVERT: C 582 PHE cc_start: 0.7382 (t80) cc_final: 0.6821 (t80) REVERT: C 590 GLU cc_start: 0.9321 (mp0) cc_final: 0.8994 (pm20) REVERT: C 634 TYR cc_start: 0.9516 (t80) cc_final: 0.9236 (t80) REVERT: C 688 LEU cc_start: 0.9507 (mm) cc_final: 0.9171 (mm) REVERT: D 28 PHE cc_start: 0.8466 (m-80) cc_final: 0.7993 (m-80) REVERT: D 38 PHE cc_start: 0.6692 (t80) cc_final: 0.6066 (t80) REVERT: D 75 MET cc_start: 0.9160 (ptm) cc_final: 0.8783 (ptm) REVERT: D 84 LEU cc_start: 0.9669 (pp) cc_final: 0.9456 (pp) REVERT: D 160 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7971 (tm-30) REVERT: D 163 LEU cc_start: 0.9711 (tt) cc_final: 0.9361 (tt) REVERT: D 164 PHE cc_start: 0.9448 (m-80) cc_final: 0.9170 (m-80) REVERT: D 198 ILE cc_start: 0.9572 (tp) cc_final: 0.9303 (mm) REVERT: D 225 GLN cc_start: 0.9122 (mp10) cc_final: 0.8867 (mp10) REVERT: D 249 TRP cc_start: 0.8693 (t-100) cc_final: 0.8434 (t-100) REVERT: D 269 HIS cc_start: 0.9138 (m-70) cc_final: 0.8736 (m-70) REVERT: D 297 MET cc_start: 0.8248 (ptm) cc_final: 0.6828 (ttm) REVERT: D 312 ASP cc_start: 0.8458 (p0) cc_final: 0.8155 (p0) REVERT: D 321 LEU cc_start: 0.8973 (mt) cc_final: 0.8740 (mt) REVERT: D 348 MET cc_start: 0.9308 (mmm) cc_final: 0.8504 (mmm) REVERT: D 418 TYR cc_start: 0.7559 (t80) cc_final: 0.7328 (t80) REVERT: E 19 GLN cc_start: 0.9637 (tt0) cc_final: 0.9063 (tm-30) REVERT: E 34 PHE cc_start: 0.9256 (t80) cc_final: 0.8891 (t80) REVERT: E 76 ILE cc_start: 0.9473 (mt) cc_final: 0.9090 (mt) REVERT: E 105 LEU cc_start: 0.8288 (mt) cc_final: 0.8027 (mt) REVERT: E 129 TYR cc_start: 0.8801 (m-10) cc_final: 0.8277 (m-10) REVERT: E 132 ASP cc_start: 0.9635 (m-30) cc_final: 0.9287 (p0) REVERT: E 133 MET cc_start: 0.8022 (mmm) cc_final: 0.7393 (mmm) REVERT: E 142 LEU cc_start: 0.9238 (mt) cc_final: 0.8973 (mt) REVERT: E 191 LEU cc_start: 0.9491 (tp) cc_final: 0.9236 (tp) REVERT: E 223 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8279 (mptt) REVERT: E 236 TYR cc_start: 0.8361 (t80) cc_final: 0.7951 (t80) REVERT: E 314 TYR cc_start: 0.8792 (t80) cc_final: 0.7980 (t80) REVERT: E 318 TYR cc_start: 0.8772 (m-10) cc_final: 0.8379 (m-10) REVERT: E 351 LEU cc_start: 0.9020 (mt) cc_final: 0.8393 (pp) REVERT: E 379 ASN cc_start: 0.9352 (t0) cc_final: 0.8709 (t0) outliers start: 1 outliers final: 1 residues processed: 395 average time/residue: 0.0880 time to fit residues: 53.2527 Evaluate side-chains 326 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 102 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN B 372 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 486 HIS C 601 HIS ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050063 restraints weight = 74478.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.051644 restraints weight = 51169.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052793 restraints weight = 38668.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053740 restraints weight = 31270.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054437 restraints weight = 26394.390| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14804 Z= 0.214 Angle : 0.770 10.124 20038 Z= 0.397 Chirality : 0.046 0.303 2295 Planarity : 0.005 0.062 2525 Dihedral : 6.576 82.285 1902 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.42 (0.20), residues: 1733 helix: -0.18 (0.16), residues: 997 sheet: -1.58 (0.45), residues: 126 loop : -1.97 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 104 TYR 0.023 0.002 TYR D 399 PHE 0.025 0.002 PHE B 492 TRP 0.029 0.002 TRP B 445 HIS 0.012 0.002 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (14804) covalent geometry : angle 0.76951 / 0.40 (20038) hydrogen bonds : bond 0.04056 / 2.70 ( 688) hydrogen bonds : angle 5.30838 / 3.76 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9412 (t80) cc_final: 0.9179 (t80) REVERT: A 784 GLU cc_start: 0.8656 (pp20) cc_final: 0.8377 (pp20) REVERT: A 816 MET cc_start: 0.9566 (ptt) cc_final: 0.9043 (pmm) REVERT: A 825 HIS cc_start: 0.9575 (m90) cc_final: 0.9155 (m90) REVERT: A 826 LEU cc_start: 0.9422 (mt) cc_final: 0.9162 (mt) REVERT: A 844 ARG cc_start: 0.8847 (mtm180) cc_final: 0.8432 (mtm-85) REVERT: A 846 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7450 (mtt180) REVERT: B 301 TRP cc_start: 0.9087 (m-10) cc_final: 0.8808 (m-10) REVERT: B 302 MET cc_start: 0.9130 (ppp) cc_final: 0.8914 (ppp) REVERT: B 303 LEU cc_start: 0.9177 (tp) cc_final: 0.8953 (tp) REVERT: B 388 LEU cc_start: 0.9135 (tp) cc_final: 0.8589 (mm) REVERT: B 393 HIS cc_start: 0.9008 (m-70) cc_final: 0.8594 (m-70) REVERT: B 426 HIS cc_start: 0.8939 (t-90) cc_final: 0.8385 (t70) REVERT: B 432 MET cc_start: 0.8395 (ptt) cc_final: 0.8054 (ptm) REVERT: C 54 MET cc_start: 0.9600 (mmp) cc_final: 0.9359 (mmm) REVERT: C 77 LEU cc_start: 0.9543 (mt) cc_final: 0.9189 (pp) REVERT: C 105 LEU cc_start: 0.9028 (tp) cc_final: 0.8728 (pt) REVERT: C 148 LEU cc_start: 0.9144 (tp) cc_final: 0.8636 (tt) REVERT: C 222 MET cc_start: 0.8478 (tmm) cc_final: 0.7975 (tmm) REVERT: C 246 LEU cc_start: 0.9149 (mt) cc_final: 0.8612 (mt) REVERT: C 330 LEU cc_start: 0.9685 (tp) cc_final: 0.9055 (tp) REVERT: C 334 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9136 (mt-10) REVERT: C 393 TYR cc_start: 0.9096 (m-80) cc_final: 0.8879 (m-80) REVERT: C 410 MET cc_start: 0.9626 (mtm) cc_final: 0.9335 (mtp) REVERT: C 582 PHE cc_start: 0.7345 (t80) cc_final: 0.6617 (t80) REVERT: C 590 GLU cc_start: 0.9384 (mp0) cc_final: 0.9067 (pm20) REVERT: C 688 LEU cc_start: 0.9598 (mm) cc_final: 0.9367 (mm) REVERT: D 28 PHE cc_start: 0.8785 (m-80) cc_final: 0.8046 (m-80) REVERT: D 38 PHE cc_start: 0.7042 (t80) cc_final: 0.6467 (t80) REVERT: D 164 PHE cc_start: 0.9484 (m-80) cc_final: 0.9198 (m-80) REVERT: D 198 ILE cc_start: 0.9571 (tp) cc_final: 0.9307 (mm) REVERT: D 225 GLN cc_start: 0.9014 (mp10) cc_final: 0.8716 (mp10) REVERT: D 269 HIS cc_start: 0.9256 (m-70) cc_final: 0.8872 (m-70) REVERT: D 312 ASP cc_start: 0.8620 (p0) cc_final: 0.8313 (p0) REVERT: D 321 LEU cc_start: 0.9062 (mt) cc_final: 0.8758 (mt) REVERT: D 339 TYR cc_start: 0.7964 (t80) cc_final: 0.7700 (t80) REVERT: D 348 MET cc_start: 0.9416 (mmm) cc_final: 0.8661 (mpp) REVERT: D 350 TYR cc_start: 0.9325 (t80) cc_final: 0.9093 (t80) REVERT: D 352 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9134 (mm-30) REVERT: D 399 TYR cc_start: 0.8702 (p90) cc_final: 0.8374 (p90) REVERT: D 401 LEU cc_start: 0.9014 (tp) cc_final: 0.8675 (tp) REVERT: E 34 PHE cc_start: 0.9367 (t80) cc_final: 0.8863 (t80) REVERT: E 105 LEU cc_start: 0.8193 (mt) cc_final: 0.7930 (mt) REVERT: E 129 TYR cc_start: 0.8932 (m-10) cc_final: 0.8578 (m-10) REVERT: E 132 ASP cc_start: 0.9625 (m-30) cc_final: 0.9366 (p0) REVERT: E 137 LEU cc_start: 0.8836 (pp) cc_final: 0.8484 (pp) REVERT: E 142 LEU cc_start: 0.9185 (mt) cc_final: 0.8934 (mt) REVERT: E 191 LEU cc_start: 0.9518 (tp) cc_final: 0.9287 (tp) REVERT: E 219 CYS cc_start: 0.7014 (t) cc_final: 0.6806 (t) REVERT: E 223 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8310 (mptt) REVERT: E 236 TYR cc_start: 0.8480 (t80) cc_final: 0.8137 (t80) REVERT: E 304 TYR cc_start: 0.9023 (t80) cc_final: 0.8573 (t80) REVERT: E 314 TYR cc_start: 0.8953 (t80) cc_final: 0.7571 (t80) REVERT: E 318 TYR cc_start: 0.8806 (m-10) cc_final: 0.8332 (m-10) REVERT: E 379 ASN cc_start: 0.9250 (t0) cc_final: 0.8676 (t0) REVERT: E 416 ILE cc_start: 0.9279 (mm) cc_final: 0.9047 (mm) outliers start: 1 outliers final: 1 residues processed: 375 average time/residue: 0.0886 time to fit residues: 50.7707 Evaluate side-chains 303 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN B 372 GLN B 542 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 378 HIS ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.066915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.050931 restraints weight = 71895.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.052504 restraints weight = 50375.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053642 restraints weight = 38607.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054535 restraints weight = 31411.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055192 restraints weight = 26729.029| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14804 Z= 0.150 Angle : 0.731 10.315 20038 Z= 0.368 Chirality : 0.045 0.284 2295 Planarity : 0.005 0.111 2525 Dihedral : 6.515 85.105 1902 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.12 % Allowed : 1.96 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.25 (0.20), residues: 1733 helix: -0.02 (0.16), residues: 1006 sheet: -1.47 (0.43), residues: 136 loop : -1.96 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 104 TYR 0.026 0.002 TYR E 304 PHE 0.025 0.002 PHE B 492 TRP 0.023 0.002 TRP B 445 HIS 0.006 0.001 HIS B 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (14804) covalent geometry : angle 0.73113 / 0.37 (20038) hydrogen bonds : bond 0.03708 / 2.45 ( 688) hydrogen bonds : angle 5.11977 / 3.62 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9381 (t80) cc_final: 0.9118 (t80) REVERT: A 781 ILE cc_start: 0.9169 (mt) cc_final: 0.8947 (mt) REVERT: A 799 TYR cc_start: 0.9317 (t80) cc_final: 0.8741 (t80) REVERT: A 816 MET cc_start: 0.9351 (ptt) cc_final: 0.8956 (pmm) REVERT: A 825 HIS cc_start: 0.9551 (m90) cc_final: 0.9146 (m90) REVERT: A 826 LEU cc_start: 0.9484 (mt) cc_final: 0.9217 (mt) REVERT: A 844 ARG cc_start: 0.8907 (mtm180) cc_final: 0.8455 (mtm-85) REVERT: B 301 TRP cc_start: 0.8940 (m-10) cc_final: 0.8711 (m-10) REVERT: B 303 LEU cc_start: 0.9188 (tp) cc_final: 0.8933 (tp) REVERT: B 330 MET cc_start: 0.8197 (mmt) cc_final: 0.7787 (mmm) REVERT: B 388 LEU cc_start: 0.9076 (tp) cc_final: 0.8570 (mm) REVERT: B 393 HIS cc_start: 0.8912 (m-70) cc_final: 0.8501 (m-70) REVERT: B 426 HIS cc_start: 0.8916 (t-90) cc_final: 0.8205 (t70) REVERT: B 432 MET cc_start: 0.8406 (ptt) cc_final: 0.8037 (ptm) REVERT: C 54 MET cc_start: 0.9590 (mmp) cc_final: 0.9368 (mmm) REVERT: C 77 LEU cc_start: 0.9492 (mt) cc_final: 0.9127 (pp) REVERT: C 148 LEU cc_start: 0.9092 (tp) cc_final: 0.8583 (tt) REVERT: C 222 MET cc_start: 0.8379 (tmm) cc_final: 0.7770 (tmm) REVERT: C 246 LEU cc_start: 0.9103 (mt) cc_final: 0.8803 (mt) REVERT: C 318 ASP cc_start: 0.9004 (t70) cc_final: 0.8784 (t70) REVERT: C 326 LYS cc_start: 0.9523 (ttmt) cc_final: 0.9315 (tttt) REVERT: C 330 LEU cc_start: 0.9683 (tp) cc_final: 0.9367 (tp) REVERT: C 334 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9089 (mt-10) REVERT: C 393 TYR cc_start: 0.9090 (m-80) cc_final: 0.8852 (m-80) REVERT: C 410 MET cc_start: 0.9633 (mtm) cc_final: 0.9312 (mtp) REVERT: C 582 PHE cc_start: 0.7240 (t80) cc_final: 0.6509 (t80) REVERT: C 590 GLU cc_start: 0.9352 (mp0) cc_final: 0.8851 (pm20) REVERT: D 28 PHE cc_start: 0.8932 (m-80) cc_final: 0.8279 (m-80) REVERT: D 38 PHE cc_start: 0.6884 (t80) cc_final: 0.6334 (t80) REVERT: D 81 LEU cc_start: 0.9585 (mt) cc_final: 0.9367 (mt) REVERT: D 198 ILE cc_start: 0.9491 (tp) cc_final: 0.9273 (mm) REVERT: D 225 GLN cc_start: 0.8992 (mp10) cc_final: 0.8689 (mp10) REVERT: D 249 TRP cc_start: 0.8732 (t-100) cc_final: 0.8418 (t-100) REVERT: D 269 HIS cc_start: 0.9214 (m-70) cc_final: 0.8789 (m-70) REVERT: D 297 MET cc_start: 0.8711 (ptm) cc_final: 0.7466 (ttm) REVERT: D 312 ASP cc_start: 0.8553 (p0) cc_final: 0.8277 (p0) REVERT: D 321 LEU cc_start: 0.9044 (mt) cc_final: 0.8831 (mt) REVERT: D 333 LYS cc_start: 0.9457 (tmmt) cc_final: 0.9075 (mtpt) REVERT: D 339 TYR cc_start: 0.8050 (t80) cc_final: 0.7781 (t80) REVERT: D 348 MET cc_start: 0.9427 (mmm) cc_final: 0.8953 (mmm) REVERT: D 350 TYR cc_start: 0.9311 (t80) cc_final: 0.8855 (t80) REVERT: D 399 TYR cc_start: 0.8656 (p90) cc_final: 0.8305 (p90) REVERT: D 401 LEU cc_start: 0.8998 (tp) cc_final: 0.8366 (tp) REVERT: D 402 MET cc_start: 0.8251 (mpp) cc_final: 0.7795 (mmm) REVERT: E 34 PHE cc_start: 0.9252 (t80) cc_final: 0.8828 (t80) REVERT: E 105 LEU cc_start: 0.8327 (mt) cc_final: 0.8088 (mt) REVERT: E 117 ASP cc_start: 0.8827 (p0) cc_final: 0.8455 (p0) REVERT: E 129 TYR cc_start: 0.8977 (m-10) cc_final: 0.8547 (m-10) REVERT: E 132 ASP cc_start: 0.9628 (m-30) cc_final: 0.9341 (p0) REVERT: E 133 MET cc_start: 0.8087 (mmm) cc_final: 0.7387 (mmm) REVERT: E 142 LEU cc_start: 0.9190 (mt) cc_final: 0.8867 (mt) REVERT: E 219 CYS cc_start: 0.6981 (t) cc_final: 0.6611 (t) REVERT: E 223 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8209 (mptt) REVERT: E 236 TYR cc_start: 0.8463 (t80) cc_final: 0.8171 (t80) REVERT: E 314 TYR cc_start: 0.8944 (t80) cc_final: 0.8165 (t80) REVERT: E 318 TYR cc_start: 0.8908 (m-10) cc_final: 0.8449 (m-10) REVERT: E 379 ASN cc_start: 0.9278 (t0) cc_final: 0.8856 (t0) outliers start: 2 outliers final: 2 residues processed: 369 average time/residue: 0.0916 time to fit residues: 51.9767 Evaluate side-chains 312 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 156 optimal weight: 0.0070 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN B 372 GLN C 52 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.067843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.051790 restraints weight = 71652.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053410 restraints weight = 49865.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054575 restraints weight = 37761.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.055502 restraints weight = 30654.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056228 restraints weight = 25931.313| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.7967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14804 Z= 0.140 Angle : 0.728 11.183 20038 Z= 0.366 Chirality : 0.045 0.285 2295 Planarity : 0.005 0.103 2525 Dihedral : 6.351 85.717 1902 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.06 % Allowed : 1.04 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.15 (0.20), residues: 1733 helix: 0.09 (0.16), residues: 998 sheet: -1.33 (0.44), residues: 136 loop : -1.98 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 830 TYR 0.028 0.001 TYR E 304 PHE 0.025 0.002 PHE B 492 TRP 0.025 0.002 TRP B 445 HIS 0.006 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14804) covalent geometry : angle 0.72775 / 0.37 (20038) hydrogen bonds : bond 0.03647 / 2.44 ( 688) hydrogen bonds : angle 5.04117 / 3.56 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 371 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9308 (t80) cc_final: 0.9050 (t80) REVERT: A 799 TYR cc_start: 0.9294 (t80) cc_final: 0.8846 (t80) REVERT: A 801 GLN cc_start: 0.9645 (mm-40) cc_final: 0.9140 (mt0) REVERT: A 816 MET cc_start: 0.9448 (ptt) cc_final: 0.9074 (pmm) REVERT: A 825 HIS cc_start: 0.9523 (m90) cc_final: 0.9211 (m90) REVERT: A 826 LEU cc_start: 0.9453 (mt) cc_final: 0.9158 (mt) REVERT: A 844 ARG cc_start: 0.8889 (mtm180) cc_final: 0.8427 (mtm-85) REVERT: B 302 MET cc_start: 0.9130 (ppp) cc_final: 0.8706 (tmm) REVERT: B 303 LEU cc_start: 0.9131 (tp) cc_final: 0.8815 (mt) REVERT: B 324 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8615 (mt-10) REVERT: B 330 MET cc_start: 0.8143 (mmt) cc_final: 0.7794 (mmm) REVERT: B 388 LEU cc_start: 0.9085 (tp) cc_final: 0.8587 (mm) REVERT: B 393 HIS cc_start: 0.8951 (m-70) cc_final: 0.8529 (m-70) REVERT: B 426 HIS cc_start: 0.8918 (t-90) cc_final: 0.8294 (t70) REVERT: B 432 MET cc_start: 0.8468 (ptt) cc_final: 0.8014 (ptm) REVERT: C 54 MET cc_start: 0.9597 (mmp) cc_final: 0.9352 (mmm) REVERT: C 77 LEU cc_start: 0.9484 (mt) cc_final: 0.9118 (pp) REVERT: C 144 MET cc_start: 0.8619 (mmp) cc_final: 0.7424 (mmp) REVERT: C 148 LEU cc_start: 0.9080 (tp) cc_final: 0.8590 (tt) REVERT: C 198 LYS cc_start: 0.9304 (mmpt) cc_final: 0.9103 (mmmt) REVERT: C 218 ILE cc_start: 0.9694 (mp) cc_final: 0.9113 (tp) REVERT: C 222 MET cc_start: 0.8298 (tmm) cc_final: 0.7708 (tmm) REVERT: C 232 ASP cc_start: 0.9118 (m-30) cc_final: 0.8811 (p0) REVERT: C 246 LEU cc_start: 0.8845 (mt) cc_final: 0.8540 (mt) REVERT: C 316 TYR cc_start: 0.8895 (m-80) cc_final: 0.8560 (m-80) REVERT: C 318 ASP cc_start: 0.9008 (t70) cc_final: 0.8492 (t70) REVERT: C 326 LYS cc_start: 0.9520 (ttmt) cc_final: 0.9246 (tttp) REVERT: C 330 LEU cc_start: 0.9673 (tp) cc_final: 0.9358 (tp) REVERT: C 334 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9088 (mt-10) REVERT: C 393 TYR cc_start: 0.9122 (m-80) cc_final: 0.8889 (m-80) REVERT: C 410 MET cc_start: 0.9621 (mtm) cc_final: 0.9357 (mtt) REVERT: C 582 PHE cc_start: 0.7269 (t80) cc_final: 0.6501 (t80) REVERT: C 590 GLU cc_start: 0.9318 (mp0) cc_final: 0.9044 (pm20) REVERT: D 28 PHE cc_start: 0.8835 (m-80) cc_final: 0.8452 (m-80) REVERT: D 38 PHE cc_start: 0.6855 (t80) cc_final: 0.6267 (t80) REVERT: D 75 MET cc_start: 0.9455 (ppp) cc_final: 0.9129 (ppp) REVERT: D 81 LEU cc_start: 0.9578 (mt) cc_final: 0.9349 (mt) REVERT: D 198 ILE cc_start: 0.9576 (tp) cc_final: 0.9239 (mm) REVERT: D 225 GLN cc_start: 0.8962 (mp10) cc_final: 0.8665 (mp10) REVERT: D 249 TRP cc_start: 0.8713 (t-100) cc_final: 0.8411 (t-100) REVERT: D 259 ASP cc_start: 0.8687 (t70) cc_final: 0.8470 (t0) REVERT: D 269 HIS cc_start: 0.9191 (m-70) cc_final: 0.8740 (m-70) REVERT: D 297 MET cc_start: 0.8609 (ptm) cc_final: 0.7366 (ttm) REVERT: D 312 ASP cc_start: 0.8549 (p0) cc_final: 0.8269 (p0) REVERT: D 321 LEU cc_start: 0.9050 (mt) cc_final: 0.8713 (mt) REVERT: D 339 TYR cc_start: 0.8047 (t80) cc_final: 0.7454 (t80) REVERT: D 350 TYR cc_start: 0.9294 (t80) cc_final: 0.8833 (t80) REVERT: D 388 MET cc_start: 0.7118 (mpp) cc_final: 0.6786 (mpp) REVERT: D 399 TYR cc_start: 0.8573 (p90) cc_final: 0.8199 (p90) REVERT: D 401 LEU cc_start: 0.8982 (tp) cc_final: 0.8450 (tp) REVERT: D 402 MET cc_start: 0.8294 (mpp) cc_final: 0.7850 (mpp) REVERT: D 418 TYR cc_start: 0.8073 (t80) cc_final: 0.7813 (t80) REVERT: E 34 PHE cc_start: 0.9239 (t80) cc_final: 0.8898 (t80) REVERT: E 96 CYS cc_start: 0.6639 (m) cc_final: 0.6321 (m) REVERT: E 117 ASP cc_start: 0.8912 (p0) cc_final: 0.8524 (p0) REVERT: E 129 TYR cc_start: 0.9058 (m-10) cc_final: 0.8651 (m-10) REVERT: E 132 ASP cc_start: 0.9576 (m-30) cc_final: 0.9340 (p0) REVERT: E 133 MET cc_start: 0.8255 (mmm) cc_final: 0.7581 (mmm) REVERT: E 223 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8322 (mmtm) REVERT: E 314 TYR cc_start: 0.8910 (t80) cc_final: 0.7832 (t80) REVERT: E 318 TYR cc_start: 0.8925 (m-10) cc_final: 0.8337 (m-10) REVERT: E 379 ASN cc_start: 0.9278 (t0) cc_final: 0.9005 (m-40) outliers start: 1 outliers final: 1 residues processed: 372 average time/residue: 0.0939 time to fit residues: 53.7387 Evaluate side-chains 313 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 32 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN C 52 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN D 378 HIS ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN E 383 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.068073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.051982 restraints weight = 72527.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.053559 restraints weight = 50871.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054750 restraints weight = 38695.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.055657 restraints weight = 31418.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056333 restraints weight = 26758.714| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.8208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14804 Z= 0.132 Angle : 0.725 10.042 20038 Z= 0.362 Chirality : 0.045 0.261 2295 Planarity : 0.005 0.097 2525 Dihedral : 6.202 88.665 1902 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.12 % Allowed : 0.80 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.15 (0.20), residues: 1733 helix: 0.08 (0.16), residues: 1006 sheet: -1.39 (0.46), residues: 125 loop : -1.98 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 104 TYR 0.030 0.002 TYR E 304 PHE 0.026 0.002 PHE B 492 TRP 0.033 0.002 TRP B 301 HIS 0.004 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14804) covalent geometry : angle 0.72487 / 0.36 (20038) hydrogen bonds : bond 0.03525 / 2.34 ( 688) hydrogen bonds : angle 4.92932 / 3.48 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9346 (t80) cc_final: 0.9089 (t80) REVERT: A 781 ILE cc_start: 0.9315 (mt) cc_final: 0.9092 (mt) REVERT: A 799 TYR cc_start: 0.9317 (t80) cc_final: 0.8848 (t80) REVERT: A 801 GLN cc_start: 0.9647 (mm-40) cc_final: 0.9172 (mt0) REVERT: A 802 HIS cc_start: 0.8947 (t70) cc_final: 0.8670 (t-90) REVERT: A 816 MET cc_start: 0.9311 (ptt) cc_final: 0.9087 (pmm) REVERT: A 825 HIS cc_start: 0.9514 (m90) cc_final: 0.9200 (m90) REVERT: A 826 LEU cc_start: 0.9453 (mt) cc_final: 0.9187 (mt) REVERT: A 844 ARG cc_start: 0.8887 (mtm180) cc_final: 0.8424 (mtm-85) REVERT: B 302 MET cc_start: 0.9111 (ppp) cc_final: 0.8907 (ppp) REVERT: B 303 LEU cc_start: 0.9143 (tp) cc_final: 0.8866 (mt) REVERT: B 324 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8496 (mt-10) REVERT: B 330 MET cc_start: 0.8297 (mmt) cc_final: 0.7901 (mmm) REVERT: B 388 LEU cc_start: 0.9100 (tp) cc_final: 0.8500 (mm) REVERT: B 393 HIS cc_start: 0.8925 (m-70) cc_final: 0.8532 (m-70) REVERT: B 426 HIS cc_start: 0.8896 (t-90) cc_final: 0.8291 (t70) REVERT: B 432 MET cc_start: 0.8514 (ptt) cc_final: 0.8054 (ptm) REVERT: C 54 MET cc_start: 0.9570 (mmp) cc_final: 0.9358 (mmm) REVERT: C 77 LEU cc_start: 0.9467 (mt) cc_final: 0.9120 (pp) REVERT: C 144 MET cc_start: 0.8953 (mmp) cc_final: 0.7406 (mmp) REVERT: C 148 LEU cc_start: 0.9089 (tp) cc_final: 0.8580 (tt) REVERT: C 198 LYS cc_start: 0.9200 (mmpt) cc_final: 0.8965 (mmmt) REVERT: C 222 MET cc_start: 0.8272 (tmm) cc_final: 0.7661 (tmm) REVERT: C 232 ASP cc_start: 0.9126 (m-30) cc_final: 0.8805 (p0) REVERT: C 246 LEU cc_start: 0.8862 (mt) cc_final: 0.8553 (mt) REVERT: C 316 TYR cc_start: 0.8890 (m-80) cc_final: 0.8681 (m-80) REVERT: C 318 ASP cc_start: 0.9062 (t70) cc_final: 0.8548 (t70) REVERT: C 326 LYS cc_start: 0.9544 (ttmt) cc_final: 0.9257 (tttp) REVERT: C 330 LEU cc_start: 0.9696 (tp) cc_final: 0.9421 (tp) REVERT: C 334 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9108 (mt-10) REVERT: C 393 TYR cc_start: 0.9128 (m-80) cc_final: 0.8877 (m-80) REVERT: C 410 MET cc_start: 0.9637 (mtm) cc_final: 0.9343 (mtt) REVERT: C 581 TYR cc_start: 0.8117 (m-10) cc_final: 0.7855 (m-10) REVERT: C 582 PHE cc_start: 0.7282 (t80) cc_final: 0.6477 (t80) REVERT: C 590 GLU cc_start: 0.9120 (mp0) cc_final: 0.8906 (pm20) REVERT: D 28 PHE cc_start: 0.8915 (m-80) cc_final: 0.8461 (m-10) REVERT: D 38 PHE cc_start: 0.6867 (t80) cc_final: 0.6286 (t80) REVERT: D 75 MET cc_start: 0.9477 (ppp) cc_final: 0.9215 (ppp) REVERT: D 81 LEU cc_start: 0.9558 (mt) cc_final: 0.9297 (mt) REVERT: D 198 ILE cc_start: 0.9579 (tp) cc_final: 0.9282 (mm) REVERT: D 225 GLN cc_start: 0.8967 (mp10) cc_final: 0.8679 (mp10) REVERT: D 249 TRP cc_start: 0.8561 (t-100) cc_final: 0.8253 (t-100) REVERT: D 269 HIS cc_start: 0.9163 (m-70) cc_final: 0.8713 (m-70) REVERT: D 297 MET cc_start: 0.8674 (ptm) cc_final: 0.7603 (ppp) REVERT: D 302 LEU cc_start: 0.9745 (mt) cc_final: 0.9433 (mt) REVERT: D 312 ASP cc_start: 0.8528 (p0) cc_final: 0.8261 (p0) REVERT: D 321 LEU cc_start: 0.9018 (mt) cc_final: 0.8708 (mt) REVERT: D 339 TYR cc_start: 0.8117 (t80) cc_final: 0.7538 (t80) REVERT: D 348 MET cc_start: 0.9622 (mtm) cc_final: 0.9265 (mtm) REVERT: D 350 TYR cc_start: 0.9277 (t80) cc_final: 0.8809 (t80) REVERT: D 399 TYR cc_start: 0.8575 (p90) cc_final: 0.8177 (p90) REVERT: D 401 LEU cc_start: 0.8877 (tp) cc_final: 0.8522 (tp) REVERT: D 402 MET cc_start: 0.8324 (mpp) cc_final: 0.7761 (mpp) REVERT: D 418 TYR cc_start: 0.8040 (t80) cc_final: 0.7755 (t80) REVERT: D 428 TRP cc_start: 0.7751 (t-100) cc_final: 0.6599 (t-100) REVERT: E 19 GLN cc_start: 0.9659 (tt0) cc_final: 0.9034 (tm-30) REVERT: E 105 LEU cc_start: 0.8232 (mt) cc_final: 0.8005 (mt) REVERT: E 107 LYS cc_start: 0.9355 (mttm) cc_final: 0.9062 (mmmm) REVERT: E 117 ASP cc_start: 0.8930 (p0) cc_final: 0.8549 (p0) REVERT: E 129 TYR cc_start: 0.9052 (m-10) cc_final: 0.8644 (m-10) REVERT: E 132 ASP cc_start: 0.9583 (m-30) cc_final: 0.9342 (p0) REVERT: E 133 MET cc_start: 0.8239 (mmm) cc_final: 0.7531 (mmm) REVERT: E 142 LEU cc_start: 0.9367 (mt) cc_final: 0.9121 (mt) REVERT: E 164 LYS cc_start: 0.8691 (pttt) cc_final: 0.7686 (ttpp) REVERT: E 223 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8342 (mmtm) REVERT: E 314 TYR cc_start: 0.8886 (t80) cc_final: 0.7728 (t80) REVERT: E 318 TYR cc_start: 0.8891 (m-10) cc_final: 0.8314 (m-10) REVERT: E 379 ASN cc_start: 0.9276 (t0) cc_final: 0.9012 (m-40) outliers start: 2 outliers final: 2 residues processed: 369 average time/residue: 0.1006 time to fit residues: 56.5356 Evaluate side-chains 310 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.067142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.051303 restraints weight = 73595.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.052874 restraints weight = 51725.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054063 restraints weight = 39559.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054945 restraints weight = 32052.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055606 restraints weight = 27170.118| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.8387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14804 Z= 0.151 Angle : 0.738 10.256 20038 Z= 0.374 Chirality : 0.045 0.253 2295 Planarity : 0.005 0.093 2525 Dihedral : 6.165 89.189 1902 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.06 % Allowed : 0.49 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.11 (0.20), residues: 1733 helix: 0.09 (0.16), residues: 1004 sheet: -0.91 (0.45), residues: 121 loop : -2.02 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 104 TYR 0.028 0.002 TYR E 304 PHE 0.028 0.002 PHE B 492 TRP 0.061 0.003 TRP B 301 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (14804) covalent geometry : angle 0.73847 / 0.37 (20038) hydrogen bonds : bond 0.03630 / 2.44 ( 688) hydrogen bonds : angle 5.01452 / 3.54 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9386 (t80) cc_final: 0.9114 (t80) REVERT: A 781 ILE cc_start: 0.9204 (mt) cc_final: 0.8885 (mt) REVERT: A 784 GLU cc_start: 0.8435 (pp20) cc_final: 0.8003 (pp20) REVERT: A 799 TYR cc_start: 0.9384 (t80) cc_final: 0.8892 (t80) REVERT: A 801 GLN cc_start: 0.9672 (mm-40) cc_final: 0.9149 (mt0) REVERT: A 816 MET cc_start: 0.9324 (ptt) cc_final: 0.9093 (pmm) REVERT: A 825 HIS cc_start: 0.9503 (m90) cc_final: 0.9203 (m90) REVERT: A 826 LEU cc_start: 0.9435 (mt) cc_final: 0.9150 (mt) REVERT: A 840 ASP cc_start: 0.8786 (t70) cc_final: 0.8547 (t0) REVERT: A 844 ARG cc_start: 0.8898 (mtm180) cc_final: 0.8463 (mtm-85) REVERT: B 324 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8460 (mt-10) REVERT: B 388 LEU cc_start: 0.8970 (tp) cc_final: 0.8463 (mm) REVERT: B 393 HIS cc_start: 0.8825 (m-70) cc_final: 0.8281 (m-70) REVERT: B 426 HIS cc_start: 0.8957 (t-90) cc_final: 0.8329 (t70) REVERT: B 432 MET cc_start: 0.8518 (ptt) cc_final: 0.8127 (ptm) REVERT: B 440 LEU cc_start: 0.9487 (mm) cc_final: 0.8847 (tp) REVERT: C 54 MET cc_start: 0.9572 (mmp) cc_final: 0.9362 (mmm) REVERT: C 77 LEU cc_start: 0.9491 (mt) cc_final: 0.9138 (pp) REVERT: C 144 MET cc_start: 0.8964 (mmp) cc_final: 0.7450 (mmp) REVERT: C 148 LEU cc_start: 0.9095 (tp) cc_final: 0.8596 (tt) REVERT: C 222 MET cc_start: 0.8258 (tmm) cc_final: 0.8031 (tmm) REVERT: C 223 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8207 (mm-30) REVERT: C 232 ASP cc_start: 0.9146 (m-30) cc_final: 0.8814 (p0) REVERT: C 246 LEU cc_start: 0.8913 (mt) cc_final: 0.8589 (mt) REVERT: C 316 TYR cc_start: 0.8867 (m-80) cc_final: 0.8624 (m-80) REVERT: C 318 ASP cc_start: 0.9064 (t70) cc_final: 0.8603 (t70) REVERT: C 326 LYS cc_start: 0.9565 (ttmt) cc_final: 0.9353 (tttt) REVERT: C 330 LEU cc_start: 0.9713 (tp) cc_final: 0.9459 (tp) REVERT: C 334 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9032 (mt-10) REVERT: C 393 TYR cc_start: 0.9157 (m-80) cc_final: 0.8886 (m-80) REVERT: C 410 MET cc_start: 0.9634 (mtm) cc_final: 0.9351 (mtt) REVERT: C 582 PHE cc_start: 0.7260 (t80) cc_final: 0.6490 (t80) REVERT: D 28 PHE cc_start: 0.9077 (m-80) cc_final: 0.8694 (m-80) REVERT: D 38 PHE cc_start: 0.6941 (t80) cc_final: 0.6384 (t80) REVERT: D 75 MET cc_start: 0.9461 (ppp) cc_final: 0.9229 (ppp) REVERT: D 81 LEU cc_start: 0.9567 (mt) cc_final: 0.9311 (mt) REVERT: D 164 PHE cc_start: 0.9514 (m-80) cc_final: 0.9274 (m-80) REVERT: D 198 ILE cc_start: 0.9664 (tp) cc_final: 0.9371 (mm) REVERT: D 225 GLN cc_start: 0.8955 (mp10) cc_final: 0.8699 (mp10) REVERT: D 249 TRP cc_start: 0.8631 (t-100) cc_final: 0.8376 (t-100) REVERT: D 259 ASP cc_start: 0.7714 (m-30) cc_final: 0.7262 (m-30) REVERT: D 269 HIS cc_start: 0.9191 (m-70) cc_final: 0.8732 (m-70) REVERT: D 297 MET cc_start: 0.8732 (ptm) cc_final: 0.7632 (ttp) REVERT: D 302 LEU cc_start: 0.9744 (mt) cc_final: 0.9526 (mt) REVERT: D 312 ASP cc_start: 0.8565 (p0) cc_final: 0.8283 (p0) REVERT: D 321 LEU cc_start: 0.9061 (mt) cc_final: 0.8726 (mt) REVERT: D 339 TYR cc_start: 0.8246 (t80) cc_final: 0.7679 (t80) REVERT: D 348 MET cc_start: 0.9632 (mtm) cc_final: 0.9282 (mtm) REVERT: D 350 TYR cc_start: 0.9203 (t80) cc_final: 0.8883 (t80) REVERT: D 388 MET cc_start: 0.7171 (mpp) cc_final: 0.6690 (mpp) REVERT: D 399 TYR cc_start: 0.8610 (p90) cc_final: 0.8215 (p90) REVERT: D 401 LEU cc_start: 0.8699 (tp) cc_final: 0.8249 (tp) REVERT: D 402 MET cc_start: 0.8331 (mpp) cc_final: 0.8068 (mpp) REVERT: D 418 TYR cc_start: 0.8062 (t80) cc_final: 0.7739 (t80) REVERT: D 428 TRP cc_start: 0.7660 (t-100) cc_final: 0.6540 (t-100) REVERT: E 19 GLN cc_start: 0.9664 (tt0) cc_final: 0.9040 (tm-30) REVERT: E 34 PHE cc_start: 0.9032 (t80) cc_final: 0.8709 (t80) REVERT: E 105 LEU cc_start: 0.8239 (mt) cc_final: 0.8022 (mt) REVERT: E 107 LYS cc_start: 0.9348 (mttm) cc_final: 0.9048 (mmmm) REVERT: E 117 ASP cc_start: 0.8947 (p0) cc_final: 0.8551 (p0) REVERT: E 129 TYR cc_start: 0.9013 (m-10) cc_final: 0.8717 (m-10) REVERT: E 132 ASP cc_start: 0.9575 (m-30) cc_final: 0.9372 (p0) REVERT: E 164 LYS cc_start: 0.8777 (pttt) cc_final: 0.7847 (ttpp) REVERT: E 219 CYS cc_start: 0.7289 (t) cc_final: 0.7063 (t) REVERT: E 223 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8272 (mmtm) REVERT: E 318 TYR cc_start: 0.8820 (m-10) cc_final: 0.8182 (m-10) REVERT: E 379 ASN cc_start: 0.9281 (t0) cc_final: 0.9026 (m-40) outliers start: 1 outliers final: 1 residues processed: 362 average time/residue: 0.0964 time to fit residues: 53.2713 Evaluate side-chains 315 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 162 optimal weight: 0.0060 chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 0.0970 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN C 52 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053278 restraints weight = 71105.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054893 restraints weight = 50182.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056048 restraints weight = 38496.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056931 restraints weight = 31418.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057644 restraints weight = 26817.698| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.8582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14804 Z= 0.126 Angle : 0.741 10.411 20038 Z= 0.370 Chirality : 0.046 0.266 2295 Planarity : 0.005 0.092 2525 Dihedral : 6.007 86.219 1902 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.12 % Allowed : 0.80 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.05 (0.20), residues: 1733 helix: 0.09 (0.16), residues: 1017 sheet: -1.11 (0.48), residues: 118 loop : -1.88 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 260 TYR 0.028 0.001 TYR E 304 PHE 0.044 0.002 PHE B 298 TRP 0.096 0.003 TRP B 301 HIS 0.012 0.001 HIS C 591 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (14804) covalent geometry : angle 0.74080 / 0.37 (20038) hydrogen bonds : bond 0.03473 / 2.33 ( 688) hydrogen bonds : angle 4.87048 / 3.44 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.39 seconds wall clock time: 37 minutes 31.93 seconds (2251.93 seconds total)