Starting phenix.real_space_refine on Wed Mar 4 15:30:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ctf_30463/03_2026/7ctf_30463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ctf_30463/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ctf_30463/03_2026/7ctf_30463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ctf_30463/03_2026/7ctf_30463.map" model { file = "/net/cci-nas-00/data/ceres_data/7ctf_30463/03_2026/7ctf_30463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ctf_30463/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.12, per 1000 atoms: 0.22 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: 1.13 Conformation dependent library (CDL) restraints added in 477.2 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: 0.62 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: 2.38 Time building geometry restraints manager: 1.55 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: 7477 17.71 - 35.42: 1088 35.42 - 53.13: 333 53.13 - 70.83: 86 70.83 - 88.54: 17 Dihedral angle restraints: 9001 sinusoidal: 3731 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 8998 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: 0.280 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 18.999 88.542 5547 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 covalent geometry : bond 0.00872 (14804) covalent geometry : angle 1.36260 (20038) hydrogen bonds : bond 0.16089 ( 688) hydrogen bonds : angle 7.99072 ( 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 : 0.626 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: 0.1218 time to fit residues: 134.5723 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 : 0.520 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 E 209 ASN E 227 HIS E 266 GLN E 299 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.072173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054513 restraints weight = 66285.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056345 restraints weight = 45066.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057527 restraints weight = 33809.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058653 restraints weight = 27529.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.059494 restraints weight = 23339.092| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 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 = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14804 Z= 0.169 Angle : 0.807 13.069 20038 Z= 0.419 Chirality : 0.047 0.275 2295 Planarity : 0.006 0.075 2525 Dihedral : 9.520 84.447 1964 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.37 % Allowed : 4.67 % Favored : 94.97 % 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: -2.71 (0.18), residues: 1733 helix: -1.19 (0.15), residues: 972 sheet: -2.57 (0.36), residues: 147 loop : -2.40 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 289 TYR 0.025 0.002 TYR C 567 PHE 0.034 0.003 PHE C 559 TRP 0.032 0.003 TRP C 649 HIS 0.008 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00366 (14804) covalent geometry : angle 0.80670 (20038) hydrogen bonds : bond 0.05276 ( 688) hydrogen bonds : angle 5.72525 ( 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 526 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 520 time to evaluate : 0.599 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: 0.9298 (t80) cc_final: 0.9047 (t80) REVERT: A 795 PHE cc_start: 0.8791 (t80) cc_final: 0.8415 (t80) REVERT: A 797 GLN cc_start: 0.9312 (mt0) cc_final: 0.9005 (pt0) REVERT: A 799 TYR cc_start: 0.9136 (t80) cc_final: 0.8759 (t80) REVERT: A 801 GLN cc_start: 0.9527 (mm-40) cc_final: 0.9023 (mm110) REVERT: A 805 LEU cc_start: 0.8894 (mt) cc_final: 0.8628 (mt) REVERT: A 816 MET cc_start: 0.9308 (ptt) cc_final: 0.9097 (pmm) REVERT: A 819 THR cc_start: 0.9280 (m) cc_final: 0.8667 (p) REVERT: A 820 MET cc_start: 0.9198 (mmp) cc_final: 0.8981 (mmp) REVERT: A 825 HIS cc_start: 0.9426 (m90) cc_final: 0.9183 (m-70) REVERT: A 826 LEU cc_start: 0.9404 (mt) cc_final: 0.9022 (mt) REVERT: A 834 VAL cc_start: 0.9065 (m) cc_final: 0.8832 (p) REVERT: A 845 VAL cc_start: 0.9432 (t) cc_final: 0.9207 (p) REVERT: B 301 TRP cc_start: 0.9140 (m-10) cc_final: 0.8808 (m-10) REVERT: B 302 MET cc_start: 0.9444 (tmm) cc_final: 0.8780 (tmm) REVERT: B 303 LEU cc_start: 0.9556 (tt) cc_final: 0.9226 (tp) REVERT: B 324 GLU cc_start: 0.9008 (tp30) cc_final: 0.8277 (mt-10) REVERT: B 330 MET cc_start: 0.8090 (mtm) cc_final: 0.7879 (mmm) REVERT: B 348 VAL cc_start: 0.9475 (m) cc_final: 0.9254 (m) REVERT: B 388 LEU cc_start: 0.8965 (tp) cc_final: 0.8509 (mm) REVERT: B 394 ASN cc_start: 0.8815 (t0) cc_final: 0.8611 (t0) REVERT: B 403 GLU cc_start: 0.9319 (mp0) cc_final: 0.9097 (mp0) REVERT: B 426 HIS cc_start: 0.8965 (t-90) cc_final: 0.8373 (t70) REVERT: B 432 MET cc_start: 0.8521 (ptm) cc_final: 0.8040 (ptm) REVERT: B 434 ASP cc_start: 0.8257 (p0) cc_final: 0.7721 (p0) REVERT: B 532 LEU cc_start: 0.8780 (tp) cc_final: 0.8424 (tp) REVERT: B 536 LEU cc_start: 0.9028 (mt) cc_final: 0.8760 (pp) REVERT: C 66 ASN cc_start: 0.9151 (m-40) cc_final: 0.8161 (p0) REVERT: C 70 PHE cc_start: 0.9390 (p90) cc_final: 0.8963 (p90) REVERT: C 73 LEU cc_start: 0.9743 (tt) cc_final: 0.9498 (tt) REVERT: C 147 PHE cc_start: 0.9422 (t80) cc_final: 0.9113 (t80) REVERT: C 148 LEU cc_start: 0.9293 (tp) cc_final: 0.8996 (tt) REVERT: C 222 MET cc_start: 0.8724 (tmm) cc_final: 0.8226 (tmm) REVERT: C 232 ASP cc_start: 0.9264 (m-30) cc_final: 0.9050 (m-30) REVERT: C 314 PHE cc_start: 0.9033 (t80) cc_final: 0.8450 (t80) REVERT: C 315 LEU cc_start: 0.9750 (tp) cc_final: 0.9490 (tt) REVERT: C 318 ASP cc_start: 0.8798 (t70) cc_final: 0.8295 (t70) REVERT: C 325 ILE cc_start: 0.9701 (mt) cc_final: 0.9475 (pt) REVERT: C 326 LYS cc_start: 0.9667 (ttpt) cc_final: 0.9240 (tttt) REVERT: C 334 GLU cc_start: 0.9404 (tp30) cc_final: 0.8408 (tp30) REVERT: C 410 MET cc_start: 0.9599 (mtm) cc_final: 0.9326 (mtt) REVERT: C 581 TYR cc_start: 0.8183 (m-10) cc_final: 0.7970 (m-10) REVERT: C 582 PHE cc_start: 0.7050 (t80) cc_final: 0.5514 (t80) REVERT: C 688 LEU cc_start: 0.9621 (mm) cc_final: 0.9386 (mm) REVERT: C 693 PHE cc_start: 0.9348 (m-80) cc_final: 0.9143 (m-80) REVERT: D 38 PHE cc_start: 0.6685 (t80) cc_final: 0.6237 (t80) REVERT: D 107 ASP cc_start: 0.8617 (t0) cc_final: 0.8122 (t0) REVERT: D 155 ILE cc_start: 0.9587 (mm) cc_final: 0.9244 (tp) REVERT: D 156 PHE cc_start: 0.9570 (m-10) cc_final: 0.9324 (m-10) REVERT: D 164 PHE cc_start: 0.9451 (m-80) cc_final: 0.8963 (m-80) REVERT: D 177 PHE cc_start: 0.9354 (m-10) cc_final: 0.9133 (m-10) REVERT: D 225 GLN cc_start: 0.9298 (mp10) cc_final: 0.8967 (mp10) REVERT: D 226 TYR cc_start: 0.9472 (t80) cc_final: 0.8823 (t80) REVERT: D 282 LEU cc_start: 0.9391 (tt) cc_final: 0.9050 (tp) REVERT: D 297 MET cc_start: 0.8536 (ptm) cc_final: 0.7285 (ptm) REVERT: D 298 THR cc_start: 0.9428 (p) cc_final: 0.9204 (t) REVERT: D 302 LEU cc_start: 0.9612 (mm) cc_final: 0.9397 (mm) REVERT: D 321 LEU cc_start: 0.8974 (mt) cc_final: 0.8590 (mt) REVERT: D 330 ILE cc_start: 0.9626 (mt) cc_final: 0.9331 (mt) REVERT: D 333 LYS cc_start: 0.9402 (tmmt) cc_final: 0.8861 (mtpt) REVERT: D 339 TYR cc_start: 0.7710 (t80) cc_final: 0.7003 (t80) REVERT: D 346 PHE cc_start: 0.9291 (t80) cc_final: 0.8479 (t80) REVERT: D 378 HIS cc_start: 0.9644 (t-90) cc_final: 0.9155 (t70) REVERT: D 379 LEU cc_start: 0.9448 (tp) cc_final: 0.8973 (mp) REVERT: D 380 GLN cc_start: 0.9287 (tt0) cc_final: 0.8893 (tp40) REVERT: D 401 LEU cc_start: 0.9068 (tp) cc_final: 0.8598 (tp) REVERT: D 406 LEU cc_start: 0.8731 (mt) cc_final: 0.8371 (mt) REVERT: D 412 MET cc_start: 0.9405 (mmm) cc_final: 0.9203 (mtt) REVERT: D 418 TYR cc_start: 0.7616 (t80) cc_final: 0.7280 (t80) REVERT: E 19 GLN cc_start: 0.9617 (tt0) cc_final: 0.9215 (tm-30) REVERT: E 34 PHE cc_start: 0.9475 (t80) cc_final: 0.9189 (t80) REVERT: E 64 VAL cc_start: 0.8771 (t) cc_final: 0.8316 (t) REVERT: E 107 LYS cc_start: 0.9418 (mttm) cc_final: 0.9213 (mmmt) REVERT: E 141 PHE cc_start: 0.9065 (m-80) cc_final: 0.8466 (m-80) REVERT: E 160 ILE cc_start: 0.9152 (tp) cc_final: 0.8629 (tt) REVERT: E 172 PHE cc_start: 0.8509 (t80) cc_final: 0.8190 (t80) REVERT: E 188 GLN cc_start: 0.8118 (mt0) cc_final: 0.7905 (mt0) REVERT: E 192 SER cc_start: 0.7477 (p) cc_final: 0.6636 (t) REVERT: E 208 ILE cc_start: 0.9615 (pt) cc_final: 0.9349 (pt) REVERT: E 223 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7814 (mptt) REVERT: E 236 TYR cc_start: 0.7925 (t80) cc_final: 0.7382 (t80) REVERT: E 383 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8308 (tm-30) REVERT: E 391 GLN cc_start: 0.8532 (mm110) cc_final: 0.8305 (mm110) REVERT: E 392 LEU cc_start: 0.9169 (mt) cc_final: 0.8189 (pp) REVERT: E 409 CYS cc_start: 0.7027 (t) cc_final: 0.6611 (t) outliers start: 6 outliers final: 1 residues processed: 525 average time/residue: 0.1076 time to fit residues: 85.1779 Evaluate side-chains 381 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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: 0.0770 chunk 109 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 406 HIS C 555 ASN C 558 ASN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** 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 319 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.053817 restraints weight = 70113.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055633 restraints weight = 48817.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056944 restraints weight = 36987.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057953 restraints weight = 29860.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058697 restraints weight = 25236.868| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14804 Z= 0.153 Angle : 0.744 16.776 20038 Z= 0.378 Chirality : 0.045 0.191 2295 Planarity : 0.005 0.065 2525 Dihedral : 8.757 89.115 1964 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.18 % Allowed : 4.79 % Favored : 95.03 % 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: -0.46 (0.15), residues: 965 sheet: -2.45 (0.36), residues: 158 loop : -2.00 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 104 TYR 0.025 0.002 TYR C 567 PHE 0.029 0.002 PHE B 492 TRP 0.021 0.002 TRP C 649 HIS 0.011 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00330 (14804) covalent geometry : angle 0.74382 (20038) hydrogen bonds : bond 0.04319 ( 688) hydrogen bonds : angle 5.23998 ( 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 447 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 444 time to evaluate : 0.554 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: 0.9399 (t80) cc_final: 0.9105 (t80) REVERT: A 781 ILE cc_start: 0.9397 (mt) cc_final: 0.9182 (mt) REVERT: A 784 GLU cc_start: 0.8633 (tp30) cc_final: 0.8427 (mm-30) REVERT: A 798 ILE cc_start: 0.9725 (pt) cc_final: 0.9323 (pt) REVERT: A 801 GLN cc_start: 0.9561 (mm-40) cc_final: 0.8893 (mm-40) REVERT: A 816 MET cc_start: 0.9516 (ptt) cc_final: 0.9029 (pmm) REVERT: A 825 HIS cc_start: 0.9507 (m90) cc_final: 0.9180 (m90) REVERT: A 826 LEU cc_start: 0.9406 (mt) cc_final: 0.8946 (mt) REVERT: A 844 ARG cc_start: 0.8767 (mmt-90) cc_final: 0.8483 (mmt-90) REVERT: A 845 VAL cc_start: 0.9233 (t) cc_final: 0.9016 (p) REVERT: B 301 TRP cc_start: 0.9077 (m-10) cc_final: 0.8846 (m-10) REVERT: B 303 LEU cc_start: 0.9472 (tt) cc_final: 0.8979 (tp) REVERT: B 330 MET cc_start: 0.8079 (mtm) cc_final: 0.7805 (mmm) REVERT: B 388 LEU cc_start: 0.9052 (tp) cc_final: 0.8537 (mm) REVERT: B 394 ASN cc_start: 0.9034 (t0) cc_final: 0.8715 (t0) REVERT: B 403 GLU cc_start: 0.9364 (mp0) cc_final: 0.9016 (mp0) REVERT: B 426 HIS cc_start: 0.8993 (t-90) cc_final: 0.8530 (t70) REVERT: B 532 LEU cc_start: 0.8807 (tp) cc_final: 0.8493 (tp) REVERT: B 536 LEU cc_start: 0.9073 (mt) cc_final: 0.8805 (pp) REVERT: C 54 MET cc_start: 0.9551 (mmp) cc_final: 0.9317 (mmm) REVERT: C 66 ASN cc_start: 0.9234 (m-40) cc_final: 0.8609 (m-40) REVERT: C 77 LEU cc_start: 0.9539 (mt) cc_final: 0.9147 (pp) REVERT: C 144 MET cc_start: 0.8798 (mmp) cc_final: 0.8505 (mmm) REVERT: C 147 PHE cc_start: 0.9486 (t80) cc_final: 0.9054 (t80) REVERT: C 148 LEU cc_start: 0.9166 (tp) cc_final: 0.8877 (tt) REVERT: C 318 ASP cc_start: 0.8923 (t70) cc_final: 0.8566 (t70) REVERT: C 326 LYS cc_start: 0.9574 (ttpt) cc_final: 0.9314 (ttmt) REVERT: C 330 LEU cc_start: 0.9672 (tp) cc_final: 0.9031 (tp) REVERT: C 334 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9117 (mt-10) REVERT: C 410 MET cc_start: 0.9660 (mtm) cc_final: 0.9425 (mtt) REVERT: C 419 LEU cc_start: 0.9770 (pp) cc_final: 0.9209 (pp) REVERT: C 422 PHE cc_start: 0.9087 (m-80) cc_final: 0.8847 (m-80) REVERT: C 582 PHE cc_start: 0.6990 (t80) cc_final: 0.6305 (t80) REVERT: C 688 LEU cc_start: 0.9567 (mm) cc_final: 0.9273 (mm) REVERT: D 38 PHE cc_start: 0.6766 (t80) cc_final: 0.6191 (t80) REVERT: D 75 MET cc_start: 0.9230 (ptm) cc_final: 0.8990 (ptm) REVERT: D 107 ASP cc_start: 0.8557 (t0) cc_final: 0.8087 (t0) REVERT: D 157 ILE cc_start: 0.9483 (mp) cc_final: 0.9031 (mp) REVERT: D 158 LEU cc_start: 0.9395 (mp) cc_final: 0.9056 (tt) REVERT: D 163 LEU cc_start: 0.9594 (tt) cc_final: 0.9220 (tt) REVERT: D 164 PHE cc_start: 0.9495 (m-80) cc_final: 0.8765 (m-80) REVERT: D 198 ILE cc_start: 0.9526 (tp) cc_final: 0.9234 (mm) REVERT: D 225 GLN cc_start: 0.9140 (mp10) cc_final: 0.8902 (mp10) REVERT: D 226 TYR cc_start: 0.9432 (t80) cc_final: 0.8759 (t80) REVERT: D 233 GLN cc_start: 0.8494 (mp10) cc_final: 0.8234 (mm-40) REVERT: D 249 TRP cc_start: 0.8554 (t-100) cc_final: 0.8269 (t-100) REVERT: D 282 LEU cc_start: 0.9535 (tt) cc_final: 0.9254 (tp) REVERT: D 297 MET cc_start: 0.8674 (ptm) cc_final: 0.7649 (ptm) REVERT: D 298 THR cc_start: 0.9403 (p) cc_final: 0.9188 (t) REVERT: D 302 LEU cc_start: 0.9675 (mm) cc_final: 0.9373 (mm) REVERT: D 312 ASP cc_start: 0.8370 (p0) cc_final: 0.8054 (p0) REVERT: D 321 LEU cc_start: 0.9025 (mt) cc_final: 0.8729 (mt) REVERT: D 339 TYR cc_start: 0.7831 (t80) cc_final: 0.7161 (t80) REVERT: D 346 PHE cc_start: 0.9046 (t80) cc_final: 0.8710 (t80) REVERT: D 348 MET cc_start: 0.9266 (mmm) cc_final: 0.8224 (mmm) REVERT: D 401 LEU cc_start: 0.8885 (tp) cc_final: 0.8600 (tp) REVERT: D 406 LEU cc_start: 0.9090 (mt) cc_final: 0.8802 (mt) REVERT: E 19 GLN cc_start: 0.9640 (tt0) cc_final: 0.9024 (tm-30) REVERT: E 34 PHE cc_start: 0.9576 (t80) cc_final: 0.9230 (t80) REVERT: E 141 PHE cc_start: 0.8913 (m-80) cc_final: 0.8541 (m-80) REVERT: E 172 PHE cc_start: 0.9029 (t80) cc_final: 0.8542 (t80) REVERT: E 188 GLN cc_start: 0.7935 (mt0) cc_final: 0.7600 (mt0) REVERT: E 204 TYR cc_start: 0.8932 (t80) cc_final: 0.8582 (t80) REVERT: E 208 ILE cc_start: 0.9597 (pt) cc_final: 0.9199 (pt) REVERT: E 223 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8137 (mptt) REVERT: E 236 TYR cc_start: 0.8112 (t80) cc_final: 0.7768 (t80) REVERT: E 314 TYR cc_start: 0.8989 (t80) cc_final: 0.8017 (t80) REVERT: E 318 TYR cc_start: 0.8843 (m-10) cc_final: 0.8497 (m-10) REVERT: E 351 LEU cc_start: 0.8898 (mt) cc_final: 0.8054 (pp) REVERT: E 379 ASN cc_start: 0.9483 (t0) cc_final: 0.8862 (t0) REVERT: E 381 PHE cc_start: 0.9234 (m-10) cc_final: 0.8995 (m-80) REVERT: E 409 CYS cc_start: 0.7338 (t) cc_final: 0.7090 (t) REVERT: E 416 ILE cc_start: 0.9134 (mm) cc_final: 0.8909 (mm) outliers start: 3 outliers final: 1 residues processed: 447 average time/residue: 0.1060 time to fit residues: 71.8199 Evaluate side-chains 349 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 0.7980 chunk 157 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 GLN A 802 HIS B 304 GLN B 353 ASN B 362 HIS B 435 HIS C 58 ASN C 409 HIS C 678 HIS ** D 79 HIS ** 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 307 GLN D 396 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN E 319 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054863 restraints weight = 67914.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.056634 restraints weight = 46712.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058108 restraints weight = 34970.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.059119 restraints weight = 28156.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059880 restraints weight = 23787.616| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.6551 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= 0.129 Angle : 0.719 16.719 20038 Z= 0.360 Chirality : 0.044 0.244 2295 Planarity : 0.004 0.063 2525 Dihedral : 8.319 89.920 1964 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.18 % Allowed : 4.36 % Favored : 95.46 % 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: -1.50 (0.19), residues: 1733 helix: -0.13 (0.16), residues: 980 sheet: -2.33 (0.40), residues: 136 loop : -1.98 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 104 TYR 0.023 0.002 TYR C 567 PHE 0.028 0.002 PHE B 492 TRP 0.028 0.002 TRP B 445 HIS 0.010 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00276 (14804) covalent geometry : angle 0.71920 (20038) hydrogen bonds : bond 0.03881 ( 688) hydrogen bonds : angle 4.96914 ( 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 422 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 419 time to evaluate : 0.597 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: A 781 ILE cc_start: 0.9349 (mt) cc_final: 0.9112 (mt) REVERT: A 797 GLN cc_start: 0.9676 (mp10) cc_final: 0.9273 (mp10) REVERT: A 798 ILE cc_start: 0.9629 (pt) cc_final: 0.9097 (pt) REVERT: A 801 GLN cc_start: 0.9563 (mm-40) cc_final: 0.8769 (mm-40) REVERT: A 816 MET cc_start: 0.9531 (ptt) cc_final: 0.8794 (pmm) REVERT: A 820 MET cc_start: 0.9399 (mmp) cc_final: 0.9112 (mmm) REVERT: A 825 HIS cc_start: 0.9576 (m90) cc_final: 0.9188 (m90) REVERT: A 826 LEU cc_start: 0.9465 (mt) cc_final: 0.9032 (mt) REVERT: B 330 MET cc_start: 0.8128 (mtm) cc_final: 0.7823 (mmm) REVERT: B 378 ASN cc_start: 0.9349 (m110) cc_final: 0.9094 (m-40) REVERT: B 388 LEU cc_start: 0.9105 (tp) cc_final: 0.8493 (mt) REVERT: B 394 ASN cc_start: 0.9062 (t0) cc_final: 0.8577 (t0) REVERT: B 426 HIS cc_start: 0.8863 (t-90) cc_final: 0.8423 (t70) REVERT: B 432 MET cc_start: 0.8480 (ptm) cc_final: 0.7296 (ptm) REVERT: B 532 LEU cc_start: 0.8839 (tp) cc_final: 0.8562 (tt) REVERT: C 54 MET cc_start: 0.9519 (mmp) cc_final: 0.9298 (mmm) REVERT: C 66 ASN cc_start: 0.9363 (m-40) cc_final: 0.8401 (p0) REVERT: C 70 PHE cc_start: 0.9438 (p90) cc_final: 0.9068 (p90) REVERT: C 77 LEU cc_start: 0.9474 (mt) cc_final: 0.9103 (pp) REVERT: C 147 PHE cc_start: 0.9489 (t80) cc_final: 0.9086 (t80) REVERT: C 148 LEU cc_start: 0.9100 (tp) cc_final: 0.8757 (tt) REVERT: C 198 LYS cc_start: 0.9317 (mmpt) cc_final: 0.9098 (mmmt) REVERT: C 222 MET cc_start: 0.8042 (tmm) cc_final: 0.7825 (tmm) REVERT: C 318 ASP cc_start: 0.8955 (t70) cc_final: 0.8721 (t70) REVERT: C 326 LYS cc_start: 0.9570 (ttpt) cc_final: 0.9038 (tttp) REVERT: C 330 LEU cc_start: 0.9666 (tp) cc_final: 0.9440 (tp) REVERT: C 334 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9059 (mt-10) REVERT: C 393 TYR cc_start: 0.9273 (m-80) cc_final: 0.9024 (m-80) REVERT: C 410 MET cc_start: 0.9677 (mtm) cc_final: 0.9392 (mtt) REVERT: C 419 LEU cc_start: 0.9782 (pp) cc_final: 0.9129 (pp) REVERT: C 582 PHE cc_start: 0.7194 (t80) cc_final: 0.6522 (t80) REVERT: C 590 GLU cc_start: 0.9034 (mp0) cc_final: 0.8772 (pm20) REVERT: C 688 LEU cc_start: 0.9521 (mm) cc_final: 0.9244 (mm) REVERT: D 28 PHE cc_start: 0.8913 (m-80) cc_final: 0.8483 (m-80) REVERT: D 38 PHE cc_start: 0.6660 (t80) cc_final: 0.5972 (t80) REVERT: D 107 ASP cc_start: 0.8535 (t0) cc_final: 0.8096 (t0) REVERT: D 164 PHE cc_start: 0.9564 (m-80) cc_final: 0.9090 (m-80) REVERT: D 177 PHE cc_start: 0.9132 (m-10) cc_final: 0.8927 (m-10) REVERT: D 198 ILE cc_start: 0.9526 (tp) cc_final: 0.9263 (mm) REVERT: D 225 GLN cc_start: 0.9153 (mp10) cc_final: 0.8913 (mp10) REVERT: D 226 TYR cc_start: 0.9449 (t80) cc_final: 0.8773 (t80) REVERT: D 232 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8864 (mp0) REVERT: D 249 TRP cc_start: 0.8612 (t-100) cc_final: 0.8337 (t-100) REVERT: D 281 MET cc_start: 0.9298 (ppp) cc_final: 0.9053 (ppp) REVERT: D 282 LEU cc_start: 0.9545 (tt) cc_final: 0.9174 (tp) REVERT: D 297 MET cc_start: 0.8390 (ptm) cc_final: 0.7494 (ptm) REVERT: D 321 LEU cc_start: 0.8921 (mt) cc_final: 0.8699 (mt) REVERT: D 332 MET cc_start: 0.9659 (ptp) cc_final: 0.9458 (ptp) REVERT: D 339 TYR cc_start: 0.7796 (t80) cc_final: 0.7240 (t80) REVERT: D 346 PHE cc_start: 0.8995 (t80) cc_final: 0.8627 (t80) REVERT: D 348 MET cc_start: 0.9268 (mmm) cc_final: 0.8234 (mmm) REVERT: E 19 GLN cc_start: 0.9630 (tt0) cc_final: 0.8957 (tm-30) REVERT: E 21 LEU cc_start: 0.9364 (mt) cc_final: 0.9121 (mt) REVERT: E 34 PHE cc_start: 0.9378 (t80) cc_final: 0.9042 (t80) REVERT: E 76 ILE cc_start: 0.9524 (mt) cc_final: 0.9203 (mt) REVERT: E 129 TYR cc_start: 0.8582 (m-10) cc_final: 0.8361 (m-10) REVERT: E 141 PHE cc_start: 0.8917 (m-80) cc_final: 0.8561 (m-80) REVERT: E 188 GLN cc_start: 0.7858 (mt0) cc_final: 0.7516 (mt0) REVERT: E 236 TYR cc_start: 0.8135 (t80) cc_final: 0.7903 (t80) REVERT: E 309 ILE cc_start: 0.9606 (mm) cc_final: 0.9386 (mm) REVERT: E 314 TYR cc_start: 0.8924 (t80) cc_final: 0.7757 (t80) REVERT: E 318 TYR cc_start: 0.8573 (m-10) cc_final: 0.8249 (m-80) REVERT: E 351 LEU cc_start: 0.8932 (mt) cc_final: 0.8127 (pp) REVERT: E 379 ASN cc_start: 0.9401 (t0) cc_final: 0.8997 (t0) REVERT: E 381 PHE cc_start: 0.9278 (m-10) cc_final: 0.9057 (m-80) outliers start: 3 outliers final: 1 residues processed: 422 average time/residue: 0.1076 time to fit residues: 68.8738 Evaluate side-chains 340 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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: 9.9990 chunk 6 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 107 optimal weight: 0.0050 chunk 124 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 overall best weight: 2.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS B 304 GLN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN C 674 ASN D 79 HIS ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN E 319 ASN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.052611 restraints weight = 71527.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054309 restraints weight = 49297.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.055641 restraints weight = 37097.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056622 restraints weight = 29926.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057336 restraints weight = 25259.367| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 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 = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14804 Z= 0.167 Angle : 0.747 16.106 20038 Z= 0.378 Chirality : 0.045 0.254 2295 Planarity : 0.005 0.065 2525 Dihedral : 8.289 89.360 1964 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % 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: 0.01 (0.16), residues: 986 sheet: -1.70 (0.41), residues: 143 loop : -1.90 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 104 TYR 0.022 0.002 TYR C 47 PHE 0.027 0.002 PHE B 492 TRP 0.028 0.002 TRP B 301 HIS 0.006 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00355 (14804) covalent geometry : angle 0.74721 (20038) hydrogen bonds : bond 0.03824 ( 688) hydrogen bonds : angle 5.08255 ( 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 387 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 0.510 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 797 GLN cc_start: 0.9644 (mp10) cc_final: 0.9438 (mp10) REVERT: A 799 TYR cc_start: 0.9268 (t80) cc_final: 0.8790 (t80) REVERT: A 801 GLN cc_start: 0.9504 (mm-40) cc_final: 0.9196 (mp10) REVERT: A 802 HIS cc_start: 0.9066 (t70) cc_final: 0.8864 (t-90) REVERT: A 816 MET cc_start: 0.9591 (ptt) cc_final: 0.9026 (pmm) REVERT: A 825 HIS cc_start: 0.9598 (m90) cc_final: 0.9170 (m90) REVERT: A 826 LEU cc_start: 0.9416 (mt) cc_final: 0.9065 (mt) REVERT: B 388 LEU cc_start: 0.9167 (tp) cc_final: 0.8597 (mm) REVERT: B 393 HIS cc_start: 0.8340 (m-70) cc_final: 0.8126 (m170) REVERT: B 399 MET cc_start: 0.8972 (ptm) cc_final: 0.8633 (ptt) REVERT: B 400 LEU cc_start: 0.9736 (tp) cc_final: 0.9485 (tp) REVERT: B 426 HIS cc_start: 0.8860 (t-90) cc_final: 0.8314 (t70) REVERT: B 432 MET cc_start: 0.8564 (ptm) cc_final: 0.7734 (ptm) REVERT: B 519 GLN cc_start: 0.8423 (mt0) cc_final: 0.7957 (pt0) REVERT: C 66 ASN cc_start: 0.9454 (m-40) cc_final: 0.8492 (p0) REVERT: C 70 PHE cc_start: 0.9490 (p90) cc_final: 0.9096 (p90) REVERT: C 77 LEU cc_start: 0.9487 (mt) cc_final: 0.9136 (pp) REVERT: C 105 LEU cc_start: 0.8848 (tp) cc_final: 0.8647 (pt) REVERT: C 148 LEU cc_start: 0.9128 (tp) cc_final: 0.8626 (tt) REVERT: C 222 MET cc_start: 0.8313 (tmm) cc_final: 0.7985 (tmm) REVERT: C 318 ASP cc_start: 0.9002 (t70) cc_final: 0.8759 (t0) REVERT: C 326 LYS cc_start: 0.9596 (ttpt) cc_final: 0.9354 (ttmt) REVERT: C 330 LEU cc_start: 0.9670 (tp) cc_final: 0.9411 (tp) REVERT: C 334 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9062 (mt-10) REVERT: C 393 TYR cc_start: 0.9231 (m-80) cc_final: 0.9022 (m-80) REVERT: C 410 MET cc_start: 0.9689 (mtm) cc_final: 0.9392 (mtp) REVERT: C 582 PHE cc_start: 0.7320 (t80) cc_final: 0.6558 (t80) REVERT: C 688 LEU cc_start: 0.9505 (mm) cc_final: 0.9126 (mm) REVERT: D 28 PHE cc_start: 0.9058 (m-80) cc_final: 0.8547 (m-80) REVERT: D 38 PHE cc_start: 0.6692 (t80) cc_final: 0.5973 (t80) REVERT: D 75 MET cc_start: 0.9430 (ptt) cc_final: 0.8994 (ptm) REVERT: D 107 ASP cc_start: 0.8590 (t0) cc_final: 0.8098 (t0) REVERT: D 198 ILE cc_start: 0.9579 (tp) cc_final: 0.9286 (mm) REVERT: D 225 GLN cc_start: 0.9097 (mp10) cc_final: 0.8894 (mp10) REVERT: D 226 TYR cc_start: 0.9468 (t80) cc_final: 0.8772 (t80) REVERT: D 249 TRP cc_start: 0.8713 (t-100) cc_final: 0.8438 (t-100) REVERT: D 259 ASP cc_start: 0.8430 (t70) cc_final: 0.8168 (t0) REVERT: D 281 MET cc_start: 0.9444 (ppp) cc_final: 0.9228 (ppp) REVERT: D 297 MET cc_start: 0.8357 (ptm) cc_final: 0.7312 (ttm) REVERT: D 311 MET cc_start: 0.5783 (mpp) cc_final: 0.5332 (mmt) REVERT: D 312 ASP cc_start: 0.8400 (p0) cc_final: 0.8156 (p0) REVERT: D 321 LEU cc_start: 0.9063 (mt) cc_final: 0.8782 (mt) REVERT: D 329 ILE cc_start: 0.9611 (tp) cc_final: 0.9311 (tp) REVERT: D 330 ILE cc_start: 0.9733 (mt) cc_final: 0.9486 (mt) REVERT: D 333 LYS cc_start: 0.9428 (tmmt) cc_final: 0.9158 (mtpt) REVERT: D 339 TYR cc_start: 0.7913 (t80) cc_final: 0.7348 (t80) REVERT: D 348 MET cc_start: 0.9329 (mmm) cc_final: 0.8384 (mmm) REVERT: D 355 LYS cc_start: 0.9136 (mtmt) cc_final: 0.8863 (mttt) REVERT: E 19 GLN cc_start: 0.9660 (tt0) cc_final: 0.8972 (tm-30) REVERT: E 34 PHE cc_start: 0.9298 (t80) cc_final: 0.8981 (t80) REVERT: E 76 ILE cc_start: 0.9468 (mt) cc_final: 0.9154 (mt) REVERT: E 129 TYR cc_start: 0.8693 (m-10) cc_final: 0.8172 (m-10) REVERT: E 132 ASP cc_start: 0.9550 (m-30) cc_final: 0.9343 (p0) REVERT: E 141 PHE cc_start: 0.9063 (m-80) cc_final: 0.8807 (m-80) REVERT: E 159 GLU cc_start: 0.7607 (pp20) cc_final: 0.6910 (pp20) REVERT: E 160 ILE cc_start: 0.8721 (tt) cc_final: 0.8178 (mt) REVERT: E 188 GLN cc_start: 0.8079 (mt0) cc_final: 0.7820 (mt0) REVERT: E 236 TYR cc_start: 0.8374 (t80) cc_final: 0.8050 (t80) REVERT: E 304 TYR cc_start: 0.8974 (t80) cc_final: 0.8694 (t80) REVERT: E 314 TYR cc_start: 0.8970 (t80) cc_final: 0.7785 (t80) REVERT: E 318 TYR cc_start: 0.8771 (m-10) cc_final: 0.8469 (m-10) REVERT: E 351 LEU cc_start: 0.9080 (mt) cc_final: 0.8285 (pp) REVERT: E 379 ASN cc_start: 0.9360 (t0) cc_final: 0.8926 (t0) REVERT: E 416 ILE cc_start: 0.9192 (mm) cc_final: 0.8984 (mm) outliers start: 2 outliers final: 1 residues processed: 387 average time/residue: 0.1023 time to fit residues: 60.9332 Evaluate side-chains 327 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 0.9980 chunk 155 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 147 optimal weight: 0.0870 chunk 44 optimal weight: 9.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN B 362 HIS ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 378 HIS D 410 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN E 319 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054193 restraints weight = 69358.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056043 restraints weight = 47601.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057374 restraints weight = 35866.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058374 restraints weight = 28883.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059125 restraints weight = 24393.157| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14804 Z= 0.124 Angle : 0.718 11.718 20038 Z= 0.356 Chirality : 0.045 0.254 2295 Planarity : 0.004 0.064 2525 Dihedral : 7.977 86.158 1964 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.25 % Allowed : 3.19 % Favored : 96.56 % 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: -1.16 (0.20), residues: 1733 helix: 0.10 (0.16), residues: 992 sheet: -1.70 (0.45), residues: 126 loop : -1.91 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 104 TYR 0.021 0.002 TYR C 47 PHE 0.033 0.002 PHE A 795 TRP 0.049 0.002 TRP B 301 HIS 0.009 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00268 (14804) covalent geometry : angle 0.71845 (20038) hydrogen bonds : bond 0.03573 ( 688) hydrogen bonds : angle 4.82953 ( 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 397 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 393 time to evaluate : 0.552 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: A 777 PHE cc_start: 0.9270 (t80) cc_final: 0.8992 (t80) REVERT: A 784 GLU cc_start: 0.8119 (pp20) cc_final: 0.7868 (pp20) REVERT: A 791 GLU cc_start: 0.8437 (pm20) cc_final: 0.8227 (pm20) REVERT: A 799 TYR cc_start: 0.9024 (t80) cc_final: 0.8455 (t80) REVERT: A 816 MET cc_start: 0.9414 (ptt) cc_final: 0.9029 (pmm) REVERT: A 825 HIS cc_start: 0.9556 (m90) cc_final: 0.9193 (m90) REVERT: A 826 LEU cc_start: 0.9399 (mt) cc_final: 0.8993 (mt) REVERT: B 303 LEU cc_start: 0.9172 (tp) cc_final: 0.8967 (tp) REVERT: B 388 LEU cc_start: 0.9120 (tp) cc_final: 0.8531 (mt) REVERT: B 393 HIS cc_start: 0.9075 (m-70) cc_final: 0.8714 (m-70) REVERT: B 426 HIS cc_start: 0.8825 (t-90) cc_final: 0.8223 (t70) REVERT: B 432 MET cc_start: 0.8509 (ptm) cc_final: 0.7331 (ptm) REVERT: B 532 LEU cc_start: 0.8824 (tt) cc_final: 0.8622 (tt) REVERT: C 54 MET cc_start: 0.9565 (mmp) cc_final: 0.9339 (mmm) REVERT: C 66 ASN cc_start: 0.9404 (m-40) cc_final: 0.8437 (p0) REVERT: C 77 LEU cc_start: 0.9449 (mt) cc_final: 0.9113 (pp) REVERT: C 147 PHE cc_start: 0.9411 (t80) cc_final: 0.9014 (t80) REVERT: C 148 LEU cc_start: 0.9099 (tp) cc_final: 0.8754 (tt) REVERT: C 221 ASP cc_start: 0.9127 (t0) cc_final: 0.8875 (t0) REVERT: C 225 PHE cc_start: 0.8965 (m-80) cc_final: 0.8574 (m-80) REVERT: C 318 ASP cc_start: 0.8977 (t70) cc_final: 0.8650 (t0) REVERT: C 326 LYS cc_start: 0.9600 (ttpt) cc_final: 0.9376 (ttmt) REVERT: C 330 LEU cc_start: 0.9674 (tp) cc_final: 0.9274 (tp) REVERT: C 334 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9004 (mt-10) REVERT: C 393 TYR cc_start: 0.9270 (m-80) cc_final: 0.9000 (m-80) REVERT: C 410 MET cc_start: 0.9660 (mtm) cc_final: 0.9378 (mtp) REVERT: C 412 TYR cc_start: 0.8768 (t80) cc_final: 0.8448 (t80) REVERT: C 419 LEU cc_start: 0.9787 (pp) cc_final: 0.9239 (pp) REVERT: C 582 PHE cc_start: 0.7328 (t80) cc_final: 0.6616 (t80) REVERT: C 688 LEU cc_start: 0.9438 (mm) cc_final: 0.9130 (mm) REVERT: D 28 PHE cc_start: 0.9110 (m-80) cc_final: 0.8464 (m-80) REVERT: D 75 MET cc_start: 0.9277 (ptt) cc_final: 0.8674 (ptt) REVERT: D 104 GLN cc_start: 0.8860 (mp10) cc_final: 0.8555 (mp10) REVERT: D 169 ASN cc_start: 0.8958 (t0) cc_final: 0.8484 (p0) REVERT: D 198 ILE cc_start: 0.9586 (tp) cc_final: 0.9283 (mm) REVERT: D 226 TYR cc_start: 0.9441 (t80) cc_final: 0.8795 (t80) REVERT: D 249 TRP cc_start: 0.8686 (t-100) cc_final: 0.8476 (t-100) REVERT: D 259 ASP cc_start: 0.8567 (t70) cc_final: 0.8338 (t0) REVERT: D 269 HIS cc_start: 0.9102 (m-70) cc_final: 0.8749 (m-70) REVERT: D 321 LEU cc_start: 0.8955 (mt) cc_final: 0.8723 (mt) REVERT: D 330 ILE cc_start: 0.9684 (mt) cc_final: 0.9463 (mt) REVERT: D 333 LYS cc_start: 0.9464 (tmmt) cc_final: 0.9032 (mtpt) REVERT: D 339 TYR cc_start: 0.7964 (t80) cc_final: 0.7369 (t80) REVERT: D 346 PHE cc_start: 0.9152 (t80) cc_final: 0.8671 (t80) REVERT: D 348 MET cc_start: 0.9341 (mmm) cc_final: 0.8508 (mmm) REVERT: D 399 TYR cc_start: 0.8655 (p90) cc_final: 0.8338 (p90) REVERT: D 401 LEU cc_start: 0.8904 (tp) cc_final: 0.8584 (tp) REVERT: D 402 MET cc_start: 0.8238 (mpp) cc_final: 0.7684 (mmm) REVERT: D 412 MET cc_start: 0.9295 (mmt) cc_final: 0.9089 (mmm) REVERT: E 19 GLN cc_start: 0.9652 (tt0) cc_final: 0.8979 (tm-30) REVERT: E 34 PHE cc_start: 0.9217 (t80) cc_final: 0.8866 (t80) REVERT: E 105 LEU cc_start: 0.8241 (mt) cc_final: 0.8024 (mt) REVERT: E 129 TYR cc_start: 0.8711 (m-10) cc_final: 0.8062 (m-10) REVERT: E 132 ASP cc_start: 0.9591 (m-30) cc_final: 0.9327 (p0) REVERT: E 133 MET cc_start: 0.7973 (mmm) cc_final: 0.7274 (mmm) REVERT: E 160 ILE cc_start: 0.8800 (tt) cc_final: 0.8287 (mt) REVERT: E 188 GLN cc_start: 0.8015 (mt0) cc_final: 0.7754 (mt0) REVERT: E 314 TYR cc_start: 0.8946 (t80) cc_final: 0.7984 (t80) REVERT: E 318 TYR cc_start: 0.8689 (m-10) cc_final: 0.8431 (m-80) REVERT: E 351 LEU cc_start: 0.9051 (mt) cc_final: 0.8375 (pp) REVERT: E 379 ASN cc_start: 0.9344 (t0) cc_final: 0.8936 (t0) outliers start: 4 outliers final: 2 residues processed: 396 average time/residue: 0.1050 time to fit residues: 63.6222 Evaluate side-chains 332 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 103 optimal weight: 0.0060 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN E 319 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053209 restraints weight = 70128.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.055002 restraints weight = 48630.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056274 restraints weight = 36658.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057257 restraints weight = 29597.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058001 restraints weight = 24985.112| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.7632 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= 0.142 Angle : 0.717 9.551 20038 Z= 0.364 Chirality : 0.045 0.237 2295 Planarity : 0.005 0.109 2525 Dihedral : 7.812 79.246 1964 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.12 % Allowed : 2.76 % Favored : 97.11 % 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: -1.13 (0.20), residues: 1733 helix: 0.09 (0.16), residues: 997 sheet: -1.55 (0.42), residues: 139 loop : -1.88 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 104 TYR 0.026 0.002 TYR E 304 PHE 0.037 0.002 PHE B 298 TRP 0.066 0.002 TRP B 301 HIS 0.007 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00306 (14804) covalent geometry : angle 0.71680 (20038) hydrogen bonds : bond 0.03534 ( 688) hydrogen bonds : angle 4.91773 ( 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 378 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 0.559 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 773 LEU cc_start: 0.9435 (mt) cc_final: 0.9209 (mt) REVERT: A 777 PHE cc_start: 0.9442 (t80) cc_final: 0.9119 (t80) REVERT: A 784 GLU cc_start: 0.7909 (pp20) cc_final: 0.7259 (pp20) REVERT: A 798 ILE cc_start: 0.9121 (mp) cc_final: 0.8869 (mp) REVERT: A 799 TYR cc_start: 0.9117 (t80) cc_final: 0.8771 (t80) REVERT: A 801 GLN cc_start: 0.9534 (mm-40) cc_final: 0.9014 (mt0) REVERT: A 807 ARG cc_start: 0.9439 (pmt-80) cc_final: 0.9222 (pmt-80) REVERT: A 816 MET cc_start: 0.9345 (ptt) cc_final: 0.9079 (ptt) REVERT: A 825 HIS cc_start: 0.9556 (m90) cc_final: 0.9211 (m90) REVERT: A 826 LEU cc_start: 0.9387 (mt) cc_final: 0.9043 (mt) REVERT: B 303 LEU cc_start: 0.9192 (tp) cc_final: 0.8987 (tp) REVERT: B 330 MET cc_start: 0.8304 (mmp) cc_final: 0.7904 (mmp) REVERT: B 388 LEU cc_start: 0.9158 (tp) cc_final: 0.8602 (mm) REVERT: B 393 HIS cc_start: 0.9085 (m-70) cc_final: 0.8529 (m-70) REVERT: B 399 MET cc_start: 0.9146 (ptm) cc_final: 0.8808 (ptt) REVERT: B 426 HIS cc_start: 0.8869 (t-90) cc_final: 0.8205 (t70) REVERT: B 432 MET cc_start: 0.8563 (ptm) cc_final: 0.7330 (ptm) REVERT: C 54 MET cc_start: 0.9586 (mmp) cc_final: 0.9358 (mmm) REVERT: C 66 ASN cc_start: 0.9550 (m-40) cc_final: 0.8472 (p0) REVERT: C 77 LEU cc_start: 0.9461 (mt) cc_final: 0.9124 (pp) REVERT: C 133 VAL cc_start: 0.9446 (t) cc_final: 0.9126 (t) REVERT: C 148 LEU cc_start: 0.9076 (tp) cc_final: 0.8577 (tt) REVERT: C 218 ILE cc_start: 0.9691 (mp) cc_final: 0.9117 (tp) REVERT: C 279 LEU cc_start: 0.8090 (mp) cc_final: 0.7693 (tt) REVERT: C 330 LEU cc_start: 0.9681 (tp) cc_final: 0.9266 (tp) REVERT: C 334 GLU cc_start: 0.9390 (mm-30) cc_final: 0.8999 (mt-10) REVERT: C 393 TYR cc_start: 0.9189 (m-80) cc_final: 0.8953 (m-80) REVERT: C 410 MET cc_start: 0.9709 (mtm) cc_final: 0.9354 (mtp) REVERT: C 412 TYR cc_start: 0.8853 (t80) cc_final: 0.8522 (t80) REVERT: C 582 PHE cc_start: 0.7471 (t80) cc_final: 0.6726 (t80) REVERT: C 689 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8735 (pt0) REVERT: D 28 PHE cc_start: 0.9189 (m-80) cc_final: 0.8113 (m-80) REVERT: D 75 MET cc_start: 0.9152 (ptt) cc_final: 0.8419 (ptp) REVERT: D 107 ASP cc_start: 0.8848 (t0) cc_final: 0.8428 (t0) REVERT: D 169 ASN cc_start: 0.9097 (t0) cc_final: 0.8894 (t0) REVERT: D 198 ILE cc_start: 0.9572 (tp) cc_final: 0.9196 (mm) REVERT: D 269 HIS cc_start: 0.9147 (m-70) cc_final: 0.8751 (m-70) REVERT: D 297 MET cc_start: 0.8512 (ptm) cc_final: 0.7783 (ptm) REVERT: D 321 LEU cc_start: 0.9099 (mt) cc_final: 0.8728 (mt) REVERT: D 339 TYR cc_start: 0.7987 (t80) cc_final: 0.7363 (t80) REVERT: D 348 MET cc_start: 0.9368 (mmm) cc_final: 0.8540 (mmm) REVERT: D 350 TYR cc_start: 0.9340 (t80) cc_final: 0.9108 (t80) REVERT: D 399 TYR cc_start: 0.8692 (p90) cc_final: 0.8317 (p90) REVERT: D 401 LEU cc_start: 0.8919 (tp) cc_final: 0.8339 (tp) REVERT: D 402 MET cc_start: 0.8102 (mpp) cc_final: 0.7529 (mmm) REVERT: D 406 LEU cc_start: 0.9007 (mt) cc_final: 0.8772 (mt) REVERT: E 19 GLN cc_start: 0.9676 (tt0) cc_final: 0.9004 (tm-30) REVERT: E 34 PHE cc_start: 0.9207 (t80) cc_final: 0.8913 (t80) REVERT: E 76 ILE cc_start: 0.9339 (mt) cc_final: 0.8962 (mt) REVERT: E 105 LEU cc_start: 0.8314 (mt) cc_final: 0.8058 (mt) REVERT: E 129 TYR cc_start: 0.8883 (m-10) cc_final: 0.8260 (m-10) REVERT: E 132 ASP cc_start: 0.9594 (m-30) cc_final: 0.9355 (p0) REVERT: E 133 MET cc_start: 0.8072 (mmm) cc_final: 0.7337 (mmm) REVERT: E 160 ILE cc_start: 0.8808 (tt) cc_final: 0.8491 (mt) REVERT: E 188 GLN cc_start: 0.8036 (mt0) cc_final: 0.7788 (mt0) REVERT: E 204 TYR cc_start: 0.8657 (t80) cc_final: 0.8402 (t80) REVERT: E 304 TYR cc_start: 0.9043 (t80) cc_final: 0.8550 (t80) REVERT: E 314 TYR cc_start: 0.8877 (t80) cc_final: 0.8028 (t80) REVERT: E 318 TYR cc_start: 0.8758 (m-10) cc_final: 0.8367 (m-10) REVERT: E 351 LEU cc_start: 0.9000 (mt) cc_final: 0.8423 (pp) REVERT: E 379 ASN cc_start: 0.9383 (t0) cc_final: 0.9027 (t0) outliers start: 2 outliers final: 1 residues processed: 378 average time/residue: 0.0991 time to fit residues: 57.9278 Evaluate side-chains 317 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 0.0270 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 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 E 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054586 restraints weight = 70061.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056310 restraints weight = 49656.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057553 restraints weight = 38009.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058491 restraints weight = 31002.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059170 restraints weight = 26402.538| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 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 = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.7868 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 : 0.740 11.672 20038 Z= 0.369 Chirality : 0.045 0.224 2295 Planarity : 0.005 0.105 2525 Dihedral : 7.559 70.483 1964 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.12 % Allowed : 1.04 % Favored : 98.83 % 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: -1.10 (0.20), residues: 1733 helix: 0.12 (0.16), residues: 1001 sheet: -1.55 (0.45), residues: 128 loop : -1.89 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 104 TYR 0.027 0.001 TYR C 47 PHE 0.027 0.002 PHE B 492 TRP 0.085 0.003 TRP B 301 HIS 0.004 0.001 HIS B 542 Details of bonding type rmsd covalent geometry : bond 0.00277 (14804) covalent geometry : angle 0.73983 (20038) hydrogen bonds : bond 0.03588 ( 688) hydrogen bonds : angle 4.85411 ( 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 387 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 0.494 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 773 LEU cc_start: 0.9475 (mt) cc_final: 0.9272 (mt) REVERT: A 777 PHE cc_start: 0.9335 (t80) cc_final: 0.9037 (t80) REVERT: A 781 ILE cc_start: 0.9236 (mt) cc_final: 0.9012 (mt) REVERT: A 799 TYR cc_start: 0.9287 (t80) cc_final: 0.8722 (t80) REVERT: A 801 GLN cc_start: 0.9508 (mm-40) cc_final: 0.9182 (mt0) REVERT: A 816 MET cc_start: 0.9325 (ptt) cc_final: 0.8963 (pmm) REVERT: A 820 MET cc_start: 0.9573 (mmp) cc_final: 0.9347 (mmp) REVERT: A 825 HIS cc_start: 0.9550 (m90) cc_final: 0.9197 (m90) REVERT: A 826 LEU cc_start: 0.9429 (mt) cc_final: 0.9148 (mt) REVERT: B 326 PHE cc_start: 0.9422 (t80) cc_final: 0.9035 (t80) REVERT: B 388 LEU cc_start: 0.9064 (tp) cc_final: 0.8542 (mm) REVERT: B 393 HIS cc_start: 0.9009 (m-70) cc_final: 0.8475 (m-70) REVERT: B 426 HIS cc_start: 0.8832 (t-90) cc_final: 0.8165 (t70) REVERT: B 432 MET cc_start: 0.8542 (ptm) cc_final: 0.7246 (ptm) REVERT: C 54 MET cc_start: 0.9545 (mmp) cc_final: 0.9323 (mmm) REVERT: C 77 LEU cc_start: 0.9431 (mt) cc_final: 0.9092 (pp) REVERT: C 148 LEU cc_start: 0.9046 (tp) cc_final: 0.8546 (tt) REVERT: C 221 ASP cc_start: 0.9211 (t0) cc_final: 0.8877 (t0) REVERT: C 225 PHE cc_start: 0.8946 (m-80) cc_final: 0.8558 (m-80) REVERT: C 239 GLN cc_start: 0.7885 (pp30) cc_final: 0.7643 (pp30) REVERT: C 256 PRO cc_start: 0.9149 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: C 279 LEU cc_start: 0.7946 (mp) cc_final: 0.7684 (tt) REVERT: C 312 ASN cc_start: 0.9538 (t0) cc_final: 0.8970 (t0) REVERT: C 330 LEU cc_start: 0.9659 (tp) cc_final: 0.9378 (tp) REVERT: C 334 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8974 (mt-10) REVERT: C 410 MET cc_start: 0.9652 (mtm) cc_final: 0.9378 (mtt) REVERT: C 412 TYR cc_start: 0.8739 (t80) cc_final: 0.8529 (t80) REVERT: C 419 LEU cc_start: 0.9811 (pp) cc_final: 0.9377 (pp) REVERT: C 582 PHE cc_start: 0.7551 (t80) cc_final: 0.6878 (t80) REVERT: D 28 PHE cc_start: 0.8895 (m-80) cc_final: 0.8362 (m-80) REVERT: D 75 MET cc_start: 0.9063 (ptt) cc_final: 0.8317 (ptp) REVERT: D 107 ASP cc_start: 0.8850 (t0) cc_final: 0.8549 (t0) REVERT: D 169 ASN cc_start: 0.9168 (t0) cc_final: 0.8711 (p0) REVERT: D 198 ILE cc_start: 0.9570 (tp) cc_final: 0.9185 (mm) REVERT: D 249 TRP cc_start: 0.8819 (t-100) cc_final: 0.8582 (t-100) REVERT: D 269 HIS cc_start: 0.9102 (m-70) cc_final: 0.8722 (m-70) REVERT: D 282 LEU cc_start: 0.9567 (tt) cc_final: 0.9231 (tp) REVERT: D 297 MET cc_start: 0.8335 (ptm) cc_final: 0.7060 (ttm) REVERT: D 321 LEU cc_start: 0.9000 (mt) cc_final: 0.8704 (mt) REVERT: D 339 TYR cc_start: 0.7926 (t80) cc_final: 0.7379 (t80) REVERT: D 348 MET cc_start: 0.9331 (mmm) cc_final: 0.8420 (mmm) REVERT: D 350 TYR cc_start: 0.9288 (t80) cc_final: 0.9021 (t80) REVERT: D 399 TYR cc_start: 0.8545 (p90) cc_final: 0.8165 (p90) REVERT: D 401 LEU cc_start: 0.8940 (tp) cc_final: 0.8299 (tp) REVERT: D 402 MET cc_start: 0.7981 (mpp) cc_final: 0.7526 (mmm) REVERT: D 406 LEU cc_start: 0.8903 (mt) cc_final: 0.8688 (mt) REVERT: E 19 GLN cc_start: 0.9657 (tt0) cc_final: 0.8952 (tm-30) REVERT: E 34 PHE cc_start: 0.9134 (t80) cc_final: 0.8790 (t80) REVERT: E 105 LEU cc_start: 0.8245 (mt) cc_final: 0.7986 (mt) REVERT: E 129 TYR cc_start: 0.8943 (m-10) cc_final: 0.8465 (m-10) REVERT: E 132 ASP cc_start: 0.9612 (m-30) cc_final: 0.9382 (p0) REVERT: E 142 LEU cc_start: 0.9150 (mt) cc_final: 0.8839 (mt) REVERT: E 160 ILE cc_start: 0.8789 (tt) cc_final: 0.8449 (mt) REVERT: E 188 GLN cc_start: 0.8012 (mt0) cc_final: 0.7808 (mt0) REVERT: E 204 TYR cc_start: 0.8552 (t80) cc_final: 0.8285 (t80) REVERT: E 304 TYR cc_start: 0.9088 (t80) cc_final: 0.8651 (t80) REVERT: E 314 TYR cc_start: 0.8927 (t80) cc_final: 0.8400 (t80) REVERT: E 318 TYR cc_start: 0.8705 (m-10) cc_final: 0.8374 (m-10) REVERT: E 351 LEU cc_start: 0.9007 (mt) cc_final: 0.8752 (pp) REVERT: E 379 ASN cc_start: 0.9377 (t0) cc_final: 0.8857 (t0) outliers start: 2 outliers final: 1 residues processed: 387 average time/residue: 0.0985 time to fit residues: 58.7960 Evaluate side-chains 325 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS ** D 225 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 E 319 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054180 restraints weight = 71334.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.055912 restraints weight = 49391.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057167 restraints weight = 37498.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058104 restraints weight = 30379.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058824 restraints weight = 25794.773| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.8079 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= 0.139 Angle : 0.738 11.337 20038 Z= 0.373 Chirality : 0.045 0.176 2295 Planarity : 0.005 0.097 2525 Dihedral : 7.447 64.026 1964 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.12 % Allowed : 0.61 % Favored : 99.26 % 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: -1.12 (0.20), residues: 1733 helix: 0.12 (0.16), residues: 1003 sheet: -1.59 (0.44), residues: 128 loop : -1.94 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 104 TYR 0.025 0.002 TYR C 47 PHE 0.026 0.002 PHE B 492 TRP 0.082 0.003 TRP B 301 HIS 0.009 0.001 HIS C 591 Details of bonding type rmsd covalent geometry : bond 0.00302 (14804) covalent geometry : angle 0.73777 (20038) hydrogen bonds : bond 0.03575 ( 688) hydrogen bonds : angle 4.96657 ( 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 379 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 377 time to evaluate : 0.612 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: A 777 PHE cc_start: 0.9341 (t80) cc_final: 0.9047 (t80) REVERT: A 799 TYR cc_start: 0.9233 (t80) cc_final: 0.8749 (t80) REVERT: A 816 MET cc_start: 0.9376 (ptt) cc_final: 0.9068 (pmm) REVERT: A 825 HIS cc_start: 0.9534 (m90) cc_final: 0.9207 (m90) REVERT: A 826 LEU cc_start: 0.9411 (mt) cc_final: 0.9128 (mt) REVERT: B 330 MET cc_start: 0.8410 (mmp) cc_final: 0.7956 (mmm) REVERT: B 388 LEU cc_start: 0.9127 (tp) cc_final: 0.8642 (mm) REVERT: B 393 HIS cc_start: 0.9033 (m-70) cc_final: 0.8485 (m-70) REVERT: B 426 HIS cc_start: 0.8873 (t-90) cc_final: 0.8145 (t70) REVERT: B 432 MET cc_start: 0.8562 (ptm) cc_final: 0.7428 (ptm) REVERT: C 54 MET cc_start: 0.9550 (mmp) cc_final: 0.9322 (mmm) REVERT: C 77 LEU cc_start: 0.9443 (mt) cc_final: 0.9101 (pp) REVERT: C 148 LEU cc_start: 0.9095 (tp) cc_final: 0.8632 (tt) REVERT: C 221 ASP cc_start: 0.9201 (t0) cc_final: 0.8859 (t0) REVERT: C 225 PHE cc_start: 0.8883 (m-80) cc_final: 0.8633 (m-80) REVERT: C 239 GLN cc_start: 0.7945 (pp30) cc_final: 0.7711 (pp30) REVERT: C 256 PRO cc_start: 0.9173 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: C 279 LEU cc_start: 0.8075 (mp) cc_final: 0.7717 (tt) REVERT: C 313 ILE cc_start: 0.9490 (pt) cc_final: 0.9099 (pt) REVERT: C 317 HIS cc_start: 0.9339 (m90) cc_final: 0.8174 (m90) REVERT: C 318 ASP cc_start: 0.8696 (t70) cc_final: 0.8293 (t70) REVERT: C 330 LEU cc_start: 0.9660 (tp) cc_final: 0.9341 (tp) REVERT: C 334 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8961 (mt-10) REVERT: C 393 TYR cc_start: 0.9164 (m-80) cc_final: 0.8939 (m-80) REVERT: C 410 MET cc_start: 0.9643 (mtm) cc_final: 0.9367 (mtt) REVERT: C 412 TYR cc_start: 0.9011 (t80) cc_final: 0.8654 (t80) REVERT: C 581 TYR cc_start: 0.8323 (m-10) cc_final: 0.8051 (m-10) REVERT: C 582 PHE cc_start: 0.7478 (t80) cc_final: 0.6690 (t80) REVERT: D 28 PHE cc_start: 0.8894 (m-80) cc_final: 0.8494 (m-80) REVERT: D 75 MET cc_start: 0.9081 (ptt) cc_final: 0.8499 (ptp) REVERT: D 107 ASP cc_start: 0.8755 (t0) cc_final: 0.8309 (t0) REVERT: D 169 ASN cc_start: 0.9150 (t0) cc_final: 0.8704 (p0) REVERT: D 198 ILE cc_start: 0.9588 (tp) cc_final: 0.9201 (mm) REVERT: D 249 TRP cc_start: 0.8600 (t-100) cc_final: 0.8351 (t-100) REVERT: D 259 ASP cc_start: 0.7584 (m-30) cc_final: 0.7154 (m-30) REVERT: D 269 HIS cc_start: 0.9093 (m-70) cc_final: 0.8725 (m-70) REVERT: D 281 MET cc_start: 0.9268 (ppp) cc_final: 0.9045 (ppp) REVERT: D 282 LEU cc_start: 0.9588 (tt) cc_final: 0.9327 (tp) REVERT: D 284 MET cc_start: 0.8539 (mmp) cc_final: 0.7903 (mmm) REVERT: D 297 MET cc_start: 0.8215 (ptm) cc_final: 0.6885 (ttm) REVERT: D 321 LEU cc_start: 0.9039 (mt) cc_final: 0.8747 (mt) REVERT: D 339 TYR cc_start: 0.8089 (t80) cc_final: 0.7573 (t80) REVERT: D 348 MET cc_start: 0.9315 (mmm) cc_final: 0.8455 (mmm) REVERT: D 350 TYR cc_start: 0.9355 (t80) cc_final: 0.9091 (t80) REVERT: D 399 TYR cc_start: 0.8697 (p90) cc_final: 0.8304 (p90) REVERT: D 401 LEU cc_start: 0.8913 (tp) cc_final: 0.8620 (tp) REVERT: D 402 MET cc_start: 0.8510 (mpp) cc_final: 0.8078 (mpp) REVERT: D 406 LEU cc_start: 0.8995 (mt) cc_final: 0.8764 (mt) REVERT: E 19 GLN cc_start: 0.9694 (tt0) cc_final: 0.9093 (tm-30) REVERT: E 34 PHE cc_start: 0.9115 (t80) cc_final: 0.8766 (t80) REVERT: E 76 ILE cc_start: 0.9268 (mt) cc_final: 0.8815 (mt) REVERT: E 105 LEU cc_start: 0.8280 (mt) cc_final: 0.8055 (mt) REVERT: E 129 TYR cc_start: 0.8986 (m-10) cc_final: 0.8549 (m-10) REVERT: E 132 ASP cc_start: 0.9631 (m-30) cc_final: 0.9383 (p0) REVERT: E 160 ILE cc_start: 0.8706 (tt) cc_final: 0.8362 (mt) REVERT: E 188 GLN cc_start: 0.8002 (mt0) cc_final: 0.7800 (mt0) REVERT: E 204 TYR cc_start: 0.8647 (t80) cc_final: 0.8349 (t80) REVERT: E 304 TYR cc_start: 0.9200 (t80) cc_final: 0.8653 (t80) REVERT: E 314 TYR cc_start: 0.8978 (t80) cc_final: 0.8218 (t80) REVERT: E 318 TYR cc_start: 0.9012 (m-10) cc_final: 0.8477 (m-10) REVERT: E 351 LEU cc_start: 0.9219 (mt) cc_final: 0.8838 (pp) REVERT: E 379 ASN cc_start: 0.9300 (t0) cc_final: 0.8798 (p0) outliers start: 2 outliers final: 1 residues processed: 379 average time/residue: 0.1021 time to fit residues: 59.8145 Evaluate side-chains 320 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 0.9990 chunk 98 optimal weight: 7.9990 chunk 175 optimal weight: 0.5980 chunk 131 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** 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 E 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.071977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055235 restraints weight = 71257.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056915 restraints weight = 50712.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058137 restraints weight = 38982.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.059088 restraints weight = 31934.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.059806 restraints weight = 27298.486| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.8282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14804 Z= 0.125 Angle : 0.741 12.976 20038 Z= 0.368 Chirality : 0.045 0.198 2295 Planarity : 0.005 0.097 2525 Dihedral : 7.159 56.089 1964 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.18 % Allowed : 0.86 % Favored : 98.96 % 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: -1.04 (0.20), residues: 1733 helix: 0.19 (0.16), residues: 998 sheet: -1.40 (0.44), residues: 120 loop : -1.93 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 493 TYR 0.025 0.001 TYR C 47 PHE 0.028 0.002 PHE B 492 TRP 0.082 0.002 TRP B 301 HIS 0.009 0.001 HIS C 591 Details of bonding type rmsd covalent geometry : bond 0.00269 (14804) covalent geometry : angle 0.74082 (20038) hydrogen bonds : bond 0.03425 ( 688) hydrogen bonds : angle 4.75826 ( 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 393 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 390 time to evaluate : 0.385 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: A 777 PHE cc_start: 0.9402 (t80) cc_final: 0.9126 (t80) REVERT: A 781 ILE cc_start: 0.9278 (mt) cc_final: 0.9075 (mt) REVERT: A 797 GLN cc_start: 0.9418 (pm20) cc_final: 0.9044 (pm20) REVERT: A 798 ILE cc_start: 0.9476 (mp) cc_final: 0.8987 (mp) REVERT: A 799 TYR cc_start: 0.9343 (t80) cc_final: 0.8881 (t80) REVERT: A 801 GLN cc_start: 0.9561 (mm-40) cc_final: 0.9085 (mt0) REVERT: A 816 MET cc_start: 0.9374 (ptt) cc_final: 0.9120 (pmm) REVERT: A 825 HIS cc_start: 0.9510 (m90) cc_final: 0.9194 (m90) REVERT: A 826 LEU cc_start: 0.9372 (mt) cc_final: 0.9125 (mt) REVERT: B 302 MET cc_start: 0.9069 (ppp) cc_final: 0.8743 (ppp) REVERT: B 303 LEU cc_start: 0.9098 (tp) cc_final: 0.8791 (mt) REVERT: B 324 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8719 (mp0) REVERT: B 326 PHE cc_start: 0.9430 (t80) cc_final: 0.9113 (t80) REVERT: B 388 LEU cc_start: 0.9104 (tp) cc_final: 0.8669 (mm) REVERT: B 393 HIS cc_start: 0.8962 (m-70) cc_final: 0.8421 (m-70) REVERT: B 399 MET cc_start: 0.8471 (ptt) cc_final: 0.8157 (ptp) REVERT: B 426 HIS cc_start: 0.8889 (t-90) cc_final: 0.8210 (t70) REVERT: B 431 LEU cc_start: 0.8932 (mm) cc_final: 0.8451 (mm) REVERT: B 437 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8751 (mmmt) REVERT: C 54 MET cc_start: 0.9537 (mmp) cc_final: 0.9337 (mmm) REVERT: C 64 GLU cc_start: 0.9377 (tm-30) cc_final: 0.9160 (tm-30) REVERT: C 65 LEU cc_start: 0.9574 (mm) cc_final: 0.8840 (mm) REVERT: C 77 LEU cc_start: 0.9513 (mt) cc_final: 0.9193 (pp) REVERT: C 148 LEU cc_start: 0.9139 (tp) cc_final: 0.8735 (tt) REVERT: C 219 LEU cc_start: 0.9518 (mp) cc_final: 0.9275 (mm) REVERT: C 221 ASP cc_start: 0.9219 (t0) cc_final: 0.9009 (t0) REVERT: C 224 SER cc_start: 0.8017 (p) cc_final: 0.7594 (p) REVERT: C 225 PHE cc_start: 0.8920 (m-80) cc_final: 0.8649 (m-80) REVERT: C 256 PRO cc_start: 0.9190 (Cg_exo) cc_final: 0.8886 (Cg_endo) REVERT: C 279 LEU cc_start: 0.8091 (mp) cc_final: 0.7843 (tt) REVERT: C 313 ILE cc_start: 0.9496 (pt) cc_final: 0.9236 (pt) REVERT: C 316 TYR cc_start: 0.8972 (m-80) cc_final: 0.8652 (m-80) REVERT: C 317 HIS cc_start: 0.9036 (m90) cc_final: 0.8792 (m90) REVERT: C 330 LEU cc_start: 0.9603 (tp) cc_final: 0.9231 (tp) REVERT: C 334 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8922 (mt-10) REVERT: C 393 TYR cc_start: 0.9125 (m-80) cc_final: 0.8901 (m-80) REVERT: C 410 MET cc_start: 0.9622 (mtm) cc_final: 0.9324 (mtt) REVERT: C 412 TYR cc_start: 0.8912 (t80) cc_final: 0.8613 (t80) REVERT: C 439 TYR cc_start: 0.8353 (t80) cc_final: 0.8120 (t80) REVERT: C 581 TYR cc_start: 0.8056 (m-10) cc_final: 0.7753 (m-10) REVERT: C 582 PHE cc_start: 0.7410 (t80) cc_final: 0.6693 (t80) REVERT: D 75 MET cc_start: 0.8997 (ptt) cc_final: 0.8405 (ptp) REVERT: D 169 ASN cc_start: 0.9138 (t0) cc_final: 0.8701 (p0) REVERT: D 194 CYS cc_start: 0.7914 (t) cc_final: 0.7500 (t) REVERT: D 198 ILE cc_start: 0.9592 (tp) cc_final: 0.9191 (mm) REVERT: D 219 ASN cc_start: 0.5259 (m110) cc_final: 0.5017 (m-40) REVERT: D 249 TRP cc_start: 0.8633 (t-100) cc_final: 0.8408 (t-100) REVERT: D 259 ASP cc_start: 0.7564 (m-30) cc_final: 0.7093 (m-30) REVERT: D 269 HIS cc_start: 0.9105 (m-70) cc_final: 0.8742 (m-70) REVERT: D 275 ASN cc_start: 0.9390 (p0) cc_final: 0.8826 (p0) REVERT: D 284 MET cc_start: 0.8532 (mmp) cc_final: 0.8301 (mmp) REVERT: D 297 MET cc_start: 0.8368 (ptm) cc_final: 0.7299 (ppp) REVERT: D 302 LEU cc_start: 0.9715 (mt) cc_final: 0.9377 (mt) REVERT: D 321 LEU cc_start: 0.9007 (mt) cc_final: 0.8743 (mt) REVERT: D 339 TYR cc_start: 0.7918 (t80) cc_final: 0.7379 (t80) REVERT: D 348 MET cc_start: 0.9313 (mmm) cc_final: 0.8455 (mmm) REVERT: D 350 TYR cc_start: 0.9314 (t80) cc_final: 0.9030 (t80) REVERT: D 388 MET cc_start: 0.7155 (mpp) cc_final: 0.6738 (mpp) REVERT: D 399 TYR cc_start: 0.8560 (p90) cc_final: 0.8263 (p90) REVERT: D 406 LEU cc_start: 0.8940 (mt) cc_final: 0.8723 (mt) REVERT: E 19 GLN cc_start: 0.9659 (tt0) cc_final: 0.8959 (tm-30) REVERT: E 21 LEU cc_start: 0.9415 (mt) cc_final: 0.9172 (mt) REVERT: E 34 PHE cc_start: 0.9010 (t80) cc_final: 0.8680 (t80) REVERT: E 105 LEU cc_start: 0.8280 (mt) cc_final: 0.8023 (mt) REVERT: E 107 LYS cc_start: 0.9334 (mttm) cc_final: 0.9100 (mmmm) REVERT: E 129 TYR cc_start: 0.9039 (m-10) cc_final: 0.8561 (m-10) REVERT: E 132 ASP cc_start: 0.9641 (m-30) cc_final: 0.9406 (p0) REVERT: E 188 GLN cc_start: 0.7927 (mt0) cc_final: 0.7687 (mt0) REVERT: E 204 TYR cc_start: 0.8550 (t80) cc_final: 0.8259 (t80) REVERT: E 314 TYR cc_start: 0.8940 (t80) cc_final: 0.8182 (t80) REVERT: E 318 TYR cc_start: 0.9004 (m-10) cc_final: 0.8589 (m-10) REVERT: E 351 LEU cc_start: 0.9214 (mt) cc_final: 0.8750 (pp) REVERT: E 379 ASN cc_start: 0.9331 (t0) cc_final: 0.8832 (t0) outliers start: 3 outliers final: 2 residues processed: 392 average time/residue: 0.1041 time to fit residues: 62.3338 Evaluate side-chains 329 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 7.9990 chunk 58 optimal weight: 0.6980 chunk 162 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN D 21 GLN ** D 225 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 E 319 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054762 restraints weight = 70862.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056386 restraints weight = 50223.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057542 restraints weight = 38836.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058443 restraints weight = 31997.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058956 restraints weight = 27382.870| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 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 = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.8462 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= 0.129 Angle : 0.739 13.298 20038 Z= 0.371 Chirality : 0.045 0.261 2295 Planarity : 0.005 0.095 2525 Dihedral : 7.097 53.874 1964 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.12 % Allowed : 0.49 % Favored : 99.39 % 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: -0.98 (0.20), residues: 1733 helix: 0.18 (0.16), residues: 1004 sheet: -1.32 (0.45), residues: 120 loop : -1.84 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 204 TYR 0.019 0.001 TYR C 47 PHE 0.028 0.002 PHE B 492 TRP 0.063 0.002 TRP B 301 HIS 0.007 0.001 HIS C 591 Details of bonding type rmsd covalent geometry : bond 0.00281 (14804) covalent geometry : angle 0.73904 (20038) hydrogen bonds : bond 0.03559 ( 688) hydrogen bonds : angle 4.74004 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2353.04 seconds wall clock time: 41 minutes 29.10 seconds (2489.10 seconds total)