Starting phenix.real_space_refine on Fri Sep 27 00:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/09_2024/7ctf_30463.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/09_2024/7ctf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/09_2024/7ctf_30463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/09_2024/7ctf_30463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/09_2024/7ctf_30463.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/09_2024/7ctf_30463.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLU:plan': 2, 'ARG:plan': 1} 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: 8.39, per 1000 atoms: 0.58 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: 5.24 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.52 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: 4.25 Time building geometry restraints manager: 5.90 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.190 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- 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= 0.559 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.044 0.004 TRP E 162 HIS 0.010 0.002 HIS D 269 PHE 0.055 0.005 PHE C 559 TYR 0.058 0.004 TYR C 609 ARG 0.008 0.001 ARG C 706 *********************** 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 fitting. rotamer outliers: 144 poor density : 684 time to evaluate : 2.107 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 THR cc_start: 0.8841 (p) cc_final: 0.8087 (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: 0.9362 (mp) REVERT: A 799 TYR cc_start: 0.9331 (t80) cc_final: 0.8868 (t80) REVERT: A 801 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8901 (mm110) REVERT: A 802 HIS cc_start: 0.8945 (t-90) cc_final: 0.8609 (t70) REVERT: A 809 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 816 MET cc_start: 0.9129 (ptt) cc_final: 0.8578 (pmm) REVERT: A 819 THR cc_start: 0.8959 (m) cc_final: 0.8168 (p) REVERT: A 834 VAL cc_start: 0.7992 (m) cc_final: 0.7595 (p) REVERT: A 838 ARG cc_start: 0.6516 (ttm-80) cc_final: 0.6282 (mtp-110) REVERT: A 847 LEU cc_start: 0.8727 (tp) cc_final: 0.8315 (tp) REVERT: B 302 MET cc_start: 0.9180 (tmm) cc_final: 0.8315 (tmm) REVERT: B 303 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8331 (tp) REVERT: B 305 LEU cc_start: 0.9194 (tp) cc_final: 0.8877 (pp) REVERT: B 327 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8749 (ttp80) REVERT: B 330 MET cc_start: 0.7848 (mtm) cc_final: 0.7531 (mmm) REVERT: B 331 LEU cc_start: 0.8867 (mp) cc_final: 0.8468 (mp) REVERT: B 335 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8664 (tp) REVERT: B 376 ILE cc_start: 0.9284 (tp) cc_final: 0.9035 (tt) REVERT: B 524 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.5937 (t80) REVERT: B 525 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7398 (mt) REVERT: B 536 LEU cc_start: 0.8858 (mt) cc_final: 0.8546 (tp) REVERT: C 47 TYR cc_start: 0.9124 (t80) cc_final: 0.8777 (t80) REVERT: C 66 ASN cc_start: 0.9344 (m-40) cc_final: 0.7812 (p0) REVERT: C 70 PHE cc_start: 0.9217 (p90) cc_final: 0.8927 (p90) REVERT: C 80 SER cc_start: 0.9468 (OUTLIER) cc_final: 0.8995 (p) REVERT: C 107 LEU cc_start: 0.9341 (mt) cc_final: 0.8905 (mt) REVERT: C 136 LEU cc_start: 0.9446 (mt) cc_final: 0.9158 (mm) REVERT: C 148 LEU cc_start: 0.9230 (tp) cc_final: 0.8770 (tt) REVERT: C 157 ASP cc_start: 0.8868 (m-30) cc_final: 0.8614 (p0) REVERT: C 162 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8195 (tp) REVERT: C 211 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: C 219 LEU cc_start: 0.9334 (mt) cc_final: 0.9133 (mt) REVERT: C 229 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8671 (p) REVERT: C 248 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8868 (pp) REVERT: C 285 LEU cc_start: 0.9413 (tp) cc_final: 0.8834 (tt) REVERT: C 314 PHE cc_start: 0.8789 (t80) cc_final: 0.8425 (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: 0.6975 (m170) REVERT: C 318 ASP cc_start: 0.8769 (t70) cc_final: 0.7990 (t70) REVERT: C 326 LYS cc_start: 0.9269 (ttpt) cc_final: 0.8958 (ttmt) REVERT: C 334 GLU cc_start: 0.8463 (tp30) cc_final: 0.7793 (tp30) REVERT: C 341 LEU cc_start: 0.7912 (mt) cc_final: 0.7513 (mt) REVERT: C 363 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8513 (t) REVERT: C 369 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7429 (tt) REVERT: C 409 HIS cc_start: 0.9405 (m-70) cc_final: 0.9125 (m-70) REVERT: C 469 MET cc_start: 0.6965 (ttm) cc_final: 0.6683 (mtt) REVERT: C 604 LEU cc_start: 0.9672 (mt) cc_final: 0.9212 (mm) REVERT: C 634 TYR cc_start: 0.9041 (t80) cc_final: 0.8541 (t80) REVERT: C 635 LYS cc_start: 0.7832 (tttt) cc_final: 0.7453 (tptt) REVERT: C 657 VAL cc_start: 0.9617 (OUTLIER) cc_final: 0.9302 (m) REVERT: C 671 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: C 674 ASN cc_start: 0.8985 (t0) cc_final: 0.8190 (m-40) REVERT: C 693 PHE cc_start: 0.8643 (m-80) cc_final: 0.8375 (m-80) REVERT: D 24 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.7153 (tt) REVERT: D 28 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.6490 (m-10) REVERT: D 64 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7659 (mt) REVERT: D 81 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.8855 (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: 0.8271 (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: 0.7945 (t0) REVERT: D 164 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7598 (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: 0.8688 (mt) REVERT: D 201 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8558 (tt) REVERT: D 226 TYR cc_start: 0.8798 (t80) cc_final: 0.8305 (t80) REVERT: D 284 MET cc_start: 0.9123 (tpt) cc_final: 0.8857 (tpp) REVERT: D 297 MET cc_start: 0.8415 (ptm) cc_final: 0.7191 (ptm) REVERT: D 326 ILE cc_start: 0.9477 (mt) cc_final: 0.9134 (mt) REVERT: D 348 MET cc_start: 0.8701 (tpt) cc_final: 0.8134 (tpt) REVERT: D 352 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8763 (mm-30) REVERT: D 377 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: D 380 GLN cc_start: 0.9023 (tt0) cc_final: 0.8607 (tm-30) REVERT: E 10 CYS cc_start: 0.7540 (m) cc_final: 0.6918 (m) REVERT: E 19 GLN cc_start: 0.9271 (tt0) cc_final: 0.8955 (tm-30) REVERT: E 21 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9068 (mt) REVERT: E 27 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7050 (p90) REVERT: E 34 PHE cc_start: 0.9455 (t80) cc_final: 0.8996 (t80) REVERT: E 35 ILE cc_start: 0.9326 (mt) cc_final: 0.8898 (mm) REVERT: E 49 THR cc_start: 0.8772 (p) cc_final: 0.8489 (p) REVERT: E 76 ILE cc_start: 0.9667 (mt) cc_final: 0.9417 (mt) REVERT: E 105 LEU cc_start: 0.8748 (mt) cc_final: 0.7820 (mt) REVERT: E 126 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8069 (tttm) REVERT: E 129 TYR cc_start: 0.8829 (m-10) cc_final: 0.7880 (m-10) REVERT: E 144 LEU cc_start: 0.9296 (tp) cc_final: 0.9007 (tt) REVERT: E 155 LEU cc_start: 0.9168 (tp) cc_final: 0.8941 (tp) REVERT: E 160 ILE cc_start: 0.9335 (tp) cc_final: 0.8624 (tt) REVERT: E 171 CYS cc_start: 0.7077 (t) cc_final: 0.6747 (t) REVERT: E 172 PHE cc_start: 0.8098 (t80) cc_final: 0.7877 (t80) REVERT: E 212 LEU cc_start: 0.9470 (tp) cc_final: 0.9247 (tp) REVERT: E 227 HIS cc_start: 0.9013 (t70) cc_final: 0.8648 (t-90) REVERT: E 253 LEU cc_start: 0.8725 (tp) cc_final: 0.8364 (mp) REVERT: E 257 ILE cc_start: 0.8418 (tp) cc_final: 0.8003 (tp) REVERT: E 307 LYS cc_start: 0.9537 (mttp) cc_final: 0.9261 (mttm) REVERT: E 314 TYR cc_start: 0.8082 (t80) cc_final: 0.7759 (t80) REVERT: E 380 ILE cc_start: 0.9065 (tp) cc_final: 0.8608 (tp) REVERT: E 401 GLN cc_start: 0.5416 (mm-40) cc_final: 0.4821 (mm-40) REVERT: E 409 CYS cc_start: 0.6693 (t) cc_final: 0.6435 (t) REVERT: E 431 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8364 (pp) outliers start: 144 outliers final: 24 residues processed: 763 average time/residue: 0.2734 time to fit residues: 298.1144 Evaluate side-chains 455 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 404 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 159 optimal weight: 0.1980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 B 306 HIS B 372 GLN B 428 ASN C 48 GLN C 146 HIS C 335 HIS C 347 ASN C 399 GLN C 555 ASN ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 307 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN E 227 HIS E 266 GLN E 299 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 14804 Z= 0.256 Angle : 0.829 12.888 20038 Z= 0.432 Chirality : 0.047 0.243 2295 Planarity : 0.006 0.072 2525 Dihedral : 9.628 84.660 1964 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.37 % Allowed : 5.16 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.18), residues: 1733 helix: -0.97 (0.15), residues: 964 sheet: -2.54 (0.37), residues: 149 loop : -2.29 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 649 HIS 0.008 0.001 HIS C 678 PHE 0.037 0.003 PHE B 492 TYR 0.024 0.002 TYR C 567 ARG 0.013 0.001 ARG D 289 *********************** 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 495 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 489 time to evaluate : 1.692 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 784 GLU cc_start: 0.8818 (tp30) cc_final: 0.8537 (mm-30) REVERT: A 795 PHE cc_start: 0.8995 (t80) cc_final: 0.8779 (t80) REVERT: A 797 GLN cc_start: 0.9425 (mt0) cc_final: 0.9004 (pt0) REVERT: A 798 ILE cc_start: 0.9646 (pt) cc_final: 0.9281 (pt) REVERT: A 799 TYR cc_start: 0.9305 (t80) cc_final: 0.8981 (t80) REVERT: A 801 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8407 (mm-40) REVERT: A 809 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8151 (tm-30) REVERT: A 816 MET cc_start: 0.9119 (ptt) cc_final: 0.8810 (pmm) REVERT: A 819 THR cc_start: 0.9056 (m) cc_final: 0.8224 (p) REVERT: A 826 LEU cc_start: 0.9044 (mt) cc_final: 0.8716 (mt) REVERT: B 302 MET cc_start: 0.9131 (tmm) cc_final: 0.8860 (ppp) REVERT: B 303 LEU cc_start: 0.9356 (tt) cc_final: 0.8820 (tp) REVERT: B 324 GLU cc_start: 0.8587 (tp30) cc_final: 0.8031 (mt-10) REVERT: B 325 ARG cc_start: 0.9290 (ptm160) cc_final: 0.9066 (ttp80) REVERT: B 426 HIS cc_start: 0.8561 (t-90) cc_final: 0.8222 (t70) REVERT: B 432 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7197 (ptm) REVERT: B 435 HIS cc_start: 0.7803 (m170) cc_final: 0.7412 (m-70) REVERT: B 493 ARG cc_start: 0.6512 (tpm170) cc_final: 0.6253 (tpm170) REVERT: B 532 LEU cc_start: 0.9006 (tp) cc_final: 0.8550 (tp) REVERT: B 536 LEU cc_start: 0.8831 (mt) cc_final: 0.8490 (pp) REVERT: C 50 ILE cc_start: 0.9506 (mt) cc_final: 0.9225 (tp) REVERT: C 66 ASN cc_start: 0.9227 (m-40) cc_final: 0.8133 (p0) REVERT: C 70 PHE cc_start: 0.9031 (p90) cc_final: 0.8817 (p90) REVERT: C 77 LEU cc_start: 0.9513 (mm) cc_final: 0.9214 (pp) REVERT: C 148 LEU cc_start: 0.9175 (tp) cc_final: 0.8828 (tt) REVERT: C 219 LEU cc_start: 0.9407 (mt) cc_final: 0.9121 (mt) REVERT: C 221 ASP cc_start: 0.8506 (t0) cc_final: 0.8194 (t0) REVERT: C 232 ASP cc_start: 0.8823 (m-30) cc_final: 0.8522 (m-30) REVERT: C 246 LEU cc_start: 0.8418 (mt) cc_final: 0.7165 (mp) REVERT: C 326 LYS cc_start: 0.9379 (ttpt) cc_final: 0.9074 (tttt) REVERT: C 334 GLU cc_start: 0.8739 (tp30) cc_final: 0.7889 (tp30) REVERT: C 363 CYS cc_start: 0.8975 (t) cc_final: 0.8716 (m) REVERT: C 410 MET cc_start: 0.9370 (mtm) cc_final: 0.9156 (mtt) REVERT: C 581 TYR cc_start: 0.7733 (m-10) cc_final: 0.7493 (m-10) REVERT: C 582 PHE cc_start: 0.6376 (t80) cc_final: 0.5322 (t80) REVERT: C 634 TYR cc_start: 0.9173 (t80) cc_final: 0.8803 (t80) REVERT: C 688 LEU cc_start: 0.9405 (mm) cc_final: 0.9199 (mm) REVERT: D 38 PHE cc_start: 0.6280 (t80) cc_final: 0.6076 (t80) REVERT: D 64 LEU cc_start: 0.9037 (tt) cc_final: 0.8828 (mm) REVERT: D 107 ASP cc_start: 0.8388 (t0) cc_final: 0.7918 (t0) REVERT: D 111 LEU cc_start: 0.9328 (mt) cc_final: 0.9127 (mt) REVERT: D 177 PHE cc_start: 0.8414 (m-10) cc_final: 0.8164 (m-10) REVERT: D 249 TRP cc_start: 0.7940 (t-100) cc_final: 0.7727 (t-100) REVERT: D 282 LEU cc_start: 0.9133 (tt) cc_final: 0.8827 (tp) REVERT: D 297 MET cc_start: 0.8502 (ptm) cc_final: 0.7608 (ptm) REVERT: D 312 ASP cc_start: 0.7745 (p0) cc_final: 0.7481 (p0) REVERT: D 321 LEU cc_start: 0.8737 (mt) cc_final: 0.8296 (mt) REVERT: D 330 ILE cc_start: 0.9506 (mt) cc_final: 0.9188 (mt) REVERT: D 333 LYS cc_start: 0.9246 (tmmt) cc_final: 0.8885 (mtpt) REVERT: D 339 TYR cc_start: 0.7331 (t80) cc_final: 0.6673 (t80) REVERT: D 346 PHE cc_start: 0.9041 (t80) cc_final: 0.8640 (t80) REVERT: D 379 LEU cc_start: 0.9465 (tp) cc_final: 0.8922 (mp) REVERT: D 388 MET cc_start: 0.8859 (mpp) cc_final: 0.8562 (mpp) REVERT: D 401 LEU cc_start: 0.8950 (tp) cc_final: 0.8508 (tp) REVERT: D 406 LEU cc_start: 0.8750 (mt) cc_final: 0.8445 (mt) REVERT: D 423 THR cc_start: 0.9214 (m) cc_final: 0.9009 (p) REVERT: E 19 GLN cc_start: 0.9474 (tt0) cc_final: 0.8944 (tm-30) REVERT: E 34 PHE cc_start: 0.9398 (t80) cc_final: 0.9178 (t80) REVERT: E 64 VAL cc_start: 0.8798 (t) cc_final: 0.8422 (t) REVERT: E 160 ILE cc_start: 0.9377 (tp) cc_final: 0.8892 (tt) REVERT: E 172 PHE cc_start: 0.8063 (t80) cc_final: 0.7694 (t80) REVERT: E 236 TYR cc_start: 0.7181 (t80) cc_final: 0.6851 (t80) REVERT: E 307 LYS cc_start: 0.9513 (mttp) cc_final: 0.9245 (mttm) REVERT: E 409 CYS cc_start: 0.6795 (t) cc_final: 0.6412 (t) outliers start: 6 outliers final: 1 residues processed: 493 average time/residue: 0.2517 time to fit residues: 182.6405 Evaluate side-chains 360 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 133 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 0.0050 chunk 158 optimal weight: 0.8980 chunk 54 optimal weight: 0.0270 chunk 128 optimal weight: 5.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 362 HIS ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS C 322 GLN C 406 HIS C 409 HIS ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14804 Z= 0.194 Angle : 0.740 15.164 20038 Z= 0.378 Chirality : 0.045 0.193 2295 Planarity : 0.005 0.067 2525 Dihedral : 8.698 86.480 1964 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.25 % Allowed : 4.36 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.19), residues: 1733 helix: -0.46 (0.16), residues: 969 sheet: -2.52 (0.38), residues: 136 loop : -2.07 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 445 HIS 0.012 0.001 HIS D 269 PHE 0.030 0.002 PHE B 492 TYR 0.027 0.002 TYR C 567 ARG 0.007 0.001 ARG E 104 *********************** 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 452 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 448 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8763 (tp30) cc_final: 0.8537 (mm-30) REVERT: A 798 ILE cc_start: 0.9651 (pt) cc_final: 0.9400 (pt) REVERT: A 799 TYR cc_start: 0.9272 (t80) cc_final: 0.9049 (t80) REVERT: A 801 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8784 (mm-40) REVERT: A 811 LEU cc_start: 0.9036 (mt) cc_final: 0.8321 (mt) REVERT: A 816 MET cc_start: 0.9073 (ptt) cc_final: 0.8648 (pmm) REVERT: A 819 THR cc_start: 0.9063 (m) cc_final: 0.8218 (p) REVERT: A 826 LEU cc_start: 0.9146 (mt) cc_final: 0.8798 (mt) REVERT: B 303 LEU cc_start: 0.9241 (tt) cc_final: 0.8749 (tp) REVERT: B 325 ARG cc_start: 0.9127 (ptm160) cc_final: 0.8763 (ptt180) REVERT: B 330 MET cc_start: 0.7879 (mtm) cc_final: 0.7623 (mmm) REVERT: B 426 HIS cc_start: 0.8736 (t-90) cc_final: 0.8308 (t70) REVERT: B 432 MET cc_start: 0.7650 (ptt) cc_final: 0.7186 (ptm) REVERT: B 435 HIS cc_start: 0.7769 (m170) cc_final: 0.7413 (m-70) REVERT: B 532 LEU cc_start: 0.9045 (tp) cc_final: 0.8428 (tt) REVERT: B 536 LEU cc_start: 0.8935 (mt) cc_final: 0.8580 (pp) REVERT: C 50 ILE cc_start: 0.9594 (mt) cc_final: 0.9314 (tp) REVERT: C 66 ASN cc_start: 0.9301 (m-40) cc_final: 0.8088 (p0) REVERT: C 70 PHE cc_start: 0.9066 (p90) cc_final: 0.8826 (p90) REVERT: C 147 PHE cc_start: 0.8950 (t80) cc_final: 0.8532 (t80) REVERT: C 148 LEU cc_start: 0.8912 (tp) cc_final: 0.8586 (tt) REVERT: C 219 LEU cc_start: 0.9356 (mt) cc_final: 0.9070 (mt) REVERT: C 326 LYS cc_start: 0.9442 (ttpt) cc_final: 0.8841 (tttp) REVERT: C 330 LEU cc_start: 0.9409 (tp) cc_final: 0.8852 (tp) REVERT: C 363 CYS cc_start: 0.8909 (t) cc_final: 0.8693 (m) REVERT: C 410 MET cc_start: 0.9429 (mtm) cc_final: 0.9170 (mtt) REVERT: C 582 PHE cc_start: 0.6128 (t80) cc_final: 0.5673 (t80) REVERT: C 688 LEU cc_start: 0.9253 (mm) cc_final: 0.8970 (mm) REVERT: C 693 PHE cc_start: 0.8958 (m-10) cc_final: 0.8516 (m-80) REVERT: D 38 PHE cc_start: 0.6137 (t80) cc_final: 0.5786 (t80) REVERT: D 158 LEU cc_start: 0.8949 (mp) cc_final: 0.8605 (mp) REVERT: D 177 PHE cc_start: 0.8370 (m-10) cc_final: 0.8166 (m-10) REVERT: D 187 ILE cc_start: 0.9523 (mt) cc_final: 0.9263 (mt) REVERT: D 232 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8771 (mp0) REVERT: D 282 LEU cc_start: 0.9326 (tt) cc_final: 0.8969 (tp) REVERT: D 297 MET cc_start: 0.8113 (ptm) cc_final: 0.7292 (ptm) REVERT: D 321 LEU cc_start: 0.8688 (mt) cc_final: 0.8261 (mt) REVERT: D 330 ILE cc_start: 0.9466 (mt) cc_final: 0.9185 (mt) REVERT: D 333 LYS cc_start: 0.9277 (tmmt) cc_final: 0.8645 (mtmt) REVERT: D 339 TYR cc_start: 0.7246 (t80) cc_final: 0.6655 (t80) REVERT: D 346 PHE cc_start: 0.8728 (t80) cc_final: 0.8384 (t80) REVERT: D 348 MET cc_start: 0.8965 (mmm) cc_final: 0.7821 (mmm) REVERT: D 379 LEU cc_start: 0.9307 (tp) cc_final: 0.9029 (mp) REVERT: D 380 GLN cc_start: 0.8756 (tp40) cc_final: 0.8260 (tp40) REVERT: D 401 LEU cc_start: 0.8736 (tp) cc_final: 0.8271 (tp) REVERT: D 406 LEU cc_start: 0.8675 (mt) cc_final: 0.8219 (mt) REVERT: E 34 PHE cc_start: 0.9502 (t80) cc_final: 0.9013 (t80) REVERT: E 126 LYS cc_start: 0.8518 (tttt) cc_final: 0.7920 (tttp) REVERT: E 129 TYR cc_start: 0.8430 (m-10) cc_final: 0.8161 (m-10) REVERT: E 159 GLU cc_start: 0.6847 (pp20) cc_final: 0.6436 (pp20) REVERT: E 172 PHE cc_start: 0.8050 (t80) cc_final: 0.7696 (t80) REVERT: E 188 GLN cc_start: 0.7835 (mt0) cc_final: 0.7503 (mt0) REVERT: E 192 SER cc_start: 0.7039 (p) cc_final: 0.6203 (t) REVERT: E 208 ILE cc_start: 0.9414 (pt) cc_final: 0.9116 (pt) REVERT: E 307 LYS cc_start: 0.9446 (mttp) cc_final: 0.9130 (mttp) REVERT: E 314 TYR cc_start: 0.8247 (t80) cc_final: 0.7967 (t80) REVERT: E 351 LEU cc_start: 0.8884 (mt) cc_final: 0.8151 (pp) REVERT: E 379 ASN cc_start: 0.9497 (t0) cc_final: 0.9293 (t0) REVERT: E 381 PHE cc_start: 0.8426 (m-10) cc_final: 0.8219 (m-80) REVERT: E 416 ILE cc_start: 0.9037 (mm) cc_final: 0.8754 (mm) outliers start: 4 outliers final: 1 residues processed: 451 average time/residue: 0.2502 time to fit residues: 167.4765 Evaluate side-chains 347 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 345 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 170 optimal weight: 0.3980 chunk 152 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 141 optimal weight: 0.0270 overall best weight: 0.8242 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 555 ASN ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14804 Z= 0.180 Angle : 0.716 16.276 20038 Z= 0.361 Chirality : 0.044 0.198 2295 Planarity : 0.004 0.062 2525 Dihedral : 7.916 86.930 1964 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.06 % Allowed : 4.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1733 helix: -0.18 (0.16), residues: 979 sheet: -2.15 (0.41), residues: 126 loop : -2.04 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 301 HIS 0.009 0.001 HIS D 269 PHE 0.038 0.002 PHE D 28 TYR 0.021 0.002 TYR D 399 ARG 0.006 0.001 ARG E 104 *********************** 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 416 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 1.846 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: A 797 GLN cc_start: 0.9652 (mp10) cc_final: 0.9173 (mp10) REVERT: A 798 ILE cc_start: 0.9664 (pt) cc_final: 0.9285 (pt) REVERT: A 799 TYR cc_start: 0.9361 (t80) cc_final: 0.8938 (t80) REVERT: A 801 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8352 (mm-40) REVERT: A 816 MET cc_start: 0.9336 (ptt) cc_final: 0.8934 (pmm) REVERT: A 819 THR cc_start: 0.9013 (m) cc_final: 0.8663 (p) REVERT: A 826 LEU cc_start: 0.9283 (mt) cc_final: 0.9035 (mt) REVERT: B 325 ARG cc_start: 0.8902 (ptm160) cc_final: 0.8338 (ptt180) REVERT: B 330 MET cc_start: 0.7984 (mtm) cc_final: 0.7765 (mmt) REVERT: B 426 HIS cc_start: 0.8520 (t-90) cc_final: 0.8242 (t70) REVERT: B 432 MET cc_start: 0.7769 (ptt) cc_final: 0.7259 (ptm) REVERT: B 435 HIS cc_start: 0.7724 (m170) cc_final: 0.7407 (m-70) REVERT: B 493 ARG cc_start: 0.6582 (tpm170) cc_final: 0.6343 (tpm170) REVERT: B 532 LEU cc_start: 0.9151 (tp) cc_final: 0.8731 (tt) REVERT: B 536 LEU cc_start: 0.8915 (mt) cc_final: 0.8588 (pp) REVERT: C 50 ILE cc_start: 0.9656 (mt) cc_final: 0.9378 (tp) REVERT: C 66 ASN cc_start: 0.9317 (m-40) cc_final: 0.7993 (p0) REVERT: C 70 PHE cc_start: 0.9109 (p90) cc_final: 0.8707 (p90) REVERT: C 77 LEU cc_start: 0.9452 (mm) cc_final: 0.9109 (pp) REVERT: C 105 LEU cc_start: 0.8845 (tp) cc_final: 0.8563 (pt) REVERT: C 144 MET cc_start: 0.7760 (mmp) cc_final: 0.6843 (mmp) REVERT: C 148 LEU cc_start: 0.8901 (tp) cc_final: 0.8486 (tt) REVERT: C 219 LEU cc_start: 0.9346 (mt) cc_final: 0.9053 (mt) REVERT: C 232 ASP cc_start: 0.8494 (m-30) cc_final: 0.8091 (p0) REVERT: C 293 LEU cc_start: 0.9228 (pt) cc_final: 0.8043 (mm) REVERT: C 326 LYS cc_start: 0.9455 (ttpt) cc_final: 0.9041 (tttt) REVERT: C 330 LEU cc_start: 0.9442 (tp) cc_final: 0.8836 (tp) REVERT: C 410 MET cc_start: 0.9420 (mtm) cc_final: 0.9190 (mtp) REVERT: C 582 PHE cc_start: 0.6059 (t80) cc_final: 0.5712 (t80) REVERT: C 688 LEU cc_start: 0.9233 (mm) cc_final: 0.8919 (mm) REVERT: D 38 PHE cc_start: 0.6004 (t80) cc_final: 0.5709 (t80) REVERT: D 198 ILE cc_start: 0.9075 (tp) cc_final: 0.8790 (mm) REVERT: D 281 MET cc_start: 0.8775 (ppp) cc_final: 0.8514 (ppp) REVERT: D 297 MET cc_start: 0.7778 (ptm) cc_final: 0.6415 (ttm) REVERT: D 321 LEU cc_start: 0.8688 (mt) cc_final: 0.8267 (mt) REVERT: D 329 ILE cc_start: 0.9564 (tp) cc_final: 0.9355 (tp) REVERT: D 339 TYR cc_start: 0.7251 (t80) cc_final: 0.6703 (t80) REVERT: D 346 PHE cc_start: 0.8751 (t80) cc_final: 0.8393 (t80) REVERT: D 348 MET cc_start: 0.9075 (mmm) cc_final: 0.7842 (mmm) REVERT: D 352 GLU cc_start: 0.9472 (mm-30) cc_final: 0.8825 (mm-30) REVERT: D 378 HIS cc_start: 0.9301 (t-90) cc_final: 0.9076 (t70) REVERT: D 380 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8472 (tm-30) REVERT: E 34 PHE cc_start: 0.9431 (t80) cc_final: 0.8615 (t80) REVERT: E 172 PHE cc_start: 0.7990 (t80) cc_final: 0.7404 (t80) REVERT: E 188 GLN cc_start: 0.7801 (mt0) cc_final: 0.7460 (mt0) REVERT: E 191 LEU cc_start: 0.9050 (tp) cc_final: 0.8687 (tp) REVERT: E 314 TYR cc_start: 0.8001 (t80) cc_final: 0.7252 (t80) REVERT: E 351 LEU cc_start: 0.8926 (mt) cc_final: 0.8122 (pp) REVERT: E 379 ASN cc_start: 0.9468 (t0) cc_final: 0.9201 (t0) REVERT: E 381 PHE cc_start: 0.8455 (m-10) cc_final: 0.8230 (m-80) outliers start: 1 outliers final: 1 residues processed: 416 average time/residue: 0.2434 time to fit residues: 151.1981 Evaluate side-chains 332 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 331 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14804 Z= 0.186 Angle : 0.727 16.530 20038 Z= 0.364 Chirality : 0.044 0.238 2295 Planarity : 0.005 0.067 2525 Dihedral : 7.826 85.247 1964 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1733 helix: -0.04 (0.16), residues: 988 sheet: -1.79 (0.42), residues: 125 loop : -2.01 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 301 HIS 0.007 0.001 HIS D 269 PHE 0.027 0.002 PHE B 492 TYR 0.020 0.002 TYR E 129 ARG 0.011 0.001 ARG E 104 *********************** 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 409 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 408 time to evaluate : 1.768 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: A 791 GLU cc_start: 0.9069 (pm20) cc_final: 0.8850 (pm20) REVERT: A 805 LEU cc_start: 0.8931 (mt) cc_final: 0.8632 (mt) REVERT: A 816 MET cc_start: 0.9502 (ptt) cc_final: 0.8919 (pmm) REVERT: A 819 THR cc_start: 0.9315 (m) cc_final: 0.8899 (p) REVERT: A 825 HIS cc_start: 0.9535 (m90) cc_final: 0.9310 (m90) REVERT: A 826 LEU cc_start: 0.9287 (mt) cc_final: 0.8993 (mt) REVERT: A 843 LEU cc_start: 0.8602 (tp) cc_final: 0.8158 (tp) REVERT: A 845 VAL cc_start: 0.8969 (m) cc_final: 0.8631 (t) REVERT: A 846 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7547 (mtt180) REVERT: B 325 ARG cc_start: 0.8943 (ptm160) cc_final: 0.8428 (ptt180) REVERT: B 330 MET cc_start: 0.7909 (mtm) cc_final: 0.7622 (mmm) REVERT: B 394 ASN cc_start: 0.8593 (t0) cc_final: 0.8300 (t0) REVERT: B 395 LEU cc_start: 0.8489 (tp) cc_final: 0.8214 (tt) REVERT: B 403 GLU cc_start: 0.8771 (mp0) cc_final: 0.8535 (mp0) REVERT: B 426 HIS cc_start: 0.8182 (t-90) cc_final: 0.7888 (t70) REVERT: B 432 MET cc_start: 0.7934 (ptt) cc_final: 0.7470 (ptm) REVERT: B 435 HIS cc_start: 0.7853 (m170) cc_final: 0.7619 (m-70) REVERT: B 493 ARG cc_start: 0.7036 (tpm170) cc_final: 0.6686 (tpm170) REVERT: B 532 LEU cc_start: 0.9184 (tp) cc_final: 0.8786 (tt) REVERT: B 536 LEU cc_start: 0.9061 (mt) cc_final: 0.8690 (pp) REVERT: C 50 ILE cc_start: 0.9652 (mt) cc_final: 0.9406 (tp) REVERT: C 66 ASN cc_start: 0.9418 (m-40) cc_final: 0.8490 (m110) REVERT: C 77 LEU cc_start: 0.9429 (mm) cc_final: 0.9124 (pp) REVERT: C 122 THR cc_start: 0.9260 (p) cc_final: 0.8398 (p) REVERT: C 148 LEU cc_start: 0.8907 (tp) cc_final: 0.8468 (tt) REVERT: C 219 LEU cc_start: 0.9276 (mt) cc_final: 0.9016 (mt) REVERT: C 293 LEU cc_start: 0.9297 (pt) cc_final: 0.8191 (mm) REVERT: C 326 LYS cc_start: 0.9473 (ttpt) cc_final: 0.9087 (tttt) REVERT: C 330 LEU cc_start: 0.9478 (tp) cc_final: 0.8812 (tp) REVERT: C 334 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8318 (mt-10) REVERT: C 410 MET cc_start: 0.9426 (mtm) cc_final: 0.9172 (mtp) REVERT: C 472 LEU cc_start: 0.9224 (mt) cc_final: 0.8973 (mt) REVERT: C 582 PHE cc_start: 0.6299 (t80) cc_final: 0.5950 (t80) REVERT: C 588 LEU cc_start: 0.9301 (tt) cc_final: 0.9035 (tt) REVERT: D 75 MET cc_start: 0.9241 (ptt) cc_final: 0.8671 (ptm) REVERT: D 107 ASP cc_start: 0.8231 (t0) cc_final: 0.7732 (t0) REVERT: D 297 MET cc_start: 0.7631 (ptm) cc_final: 0.6264 (ttm) REVERT: D 312 ASP cc_start: 0.7885 (p0) cc_final: 0.7664 (p0) REVERT: D 321 LEU cc_start: 0.8685 (mt) cc_final: 0.8219 (mt) REVERT: D 348 MET cc_start: 0.9079 (mmm) cc_final: 0.7886 (mmm) REVERT: D 352 GLU cc_start: 0.9500 (mm-30) cc_final: 0.8886 (mm-30) REVERT: D 388 MET cc_start: 0.7624 (mpp) cc_final: 0.7418 (mpp) REVERT: D 401 LEU cc_start: 0.8455 (tp) cc_final: 0.8172 (tp) REVERT: E 34 PHE cc_start: 0.9341 (t80) cc_final: 0.8853 (t80) REVERT: E 126 LYS cc_start: 0.7775 (tmtt) cc_final: 0.7364 (tptt) REVERT: E 128 GLU cc_start: 0.8905 (pm20) cc_final: 0.8537 (pm20) REVERT: E 132 ASP cc_start: 0.9326 (m-30) cc_final: 0.9023 (p0) REVERT: E 172 PHE cc_start: 0.7622 (t80) cc_final: 0.7152 (t80) REVERT: E 188 GLN cc_start: 0.8015 (mt0) cc_final: 0.7648 (mt0) REVERT: E 191 LEU cc_start: 0.9060 (tp) cc_final: 0.8668 (tp) REVERT: E 309 ILE cc_start: 0.9457 (mm) cc_final: 0.9131 (mm) REVERT: E 351 LEU cc_start: 0.8981 (mt) cc_final: 0.8239 (pp) REVERT: E 379 ASN cc_start: 0.9415 (t0) cc_final: 0.9125 (t0) outliers start: 1 outliers final: 1 residues processed: 409 average time/residue: 0.2507 time to fit residues: 153.1022 Evaluate side-chains 322 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** 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 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14804 Z= 0.181 Angle : 0.714 16.626 20038 Z= 0.356 Chirality : 0.044 0.208 2295 Planarity : 0.004 0.062 2525 Dihedral : 7.583 83.923 1964 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1733 helix: 0.16 (0.16), residues: 984 sheet: -1.65 (0.47), residues: 111 loop : -1.92 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP B 301 HIS 0.017 0.001 HIS E 27 PHE 0.025 0.002 PHE B 492 TYR 0.024 0.002 TYR E 304 ARG 0.011 0.001 ARG A 844 *********************** 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 400 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 399 time to evaluate : 1.621 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: A 784 GLU cc_start: 0.8870 (pp20) cc_final: 0.8193 (pp20) REVERT: A 791 GLU cc_start: 0.9021 (pm20) cc_final: 0.8723 (pm20) REVERT: A 816 MET cc_start: 0.9445 (ptt) cc_final: 0.9027 (pmm) REVERT: A 819 THR cc_start: 0.9189 (m) cc_final: 0.8904 (p) REVERT: A 825 HIS cc_start: 0.9494 (m90) cc_final: 0.9266 (m90) REVERT: A 826 LEU cc_start: 0.9178 (mt) cc_final: 0.8830 (mt) REVERT: B 326 PHE cc_start: 0.8956 (t80) cc_final: 0.8390 (t80) REVERT: B 330 MET cc_start: 0.8054 (mtm) cc_final: 0.7592 (mmm) REVERT: B 394 ASN cc_start: 0.8693 (t0) cc_final: 0.8482 (t0) REVERT: B 395 LEU cc_start: 0.8485 (tp) cc_final: 0.8226 (tt) REVERT: B 403 GLU cc_start: 0.8692 (mp0) cc_final: 0.8485 (mp0) REVERT: B 426 HIS cc_start: 0.8230 (t-90) cc_final: 0.7986 (t70) REVERT: B 432 MET cc_start: 0.7988 (ptt) cc_final: 0.7485 (ptm) REVERT: B 493 ARG cc_start: 0.6870 (tpm170) cc_final: 0.6564 (tpm170) REVERT: B 532 LEU cc_start: 0.9189 (tp) cc_final: 0.8790 (tt) REVERT: B 536 LEU cc_start: 0.9047 (mt) cc_final: 0.8695 (pp) REVERT: C 50 ILE cc_start: 0.9653 (mt) cc_final: 0.9420 (tp) REVERT: C 66 ASN cc_start: 0.9561 (m-40) cc_final: 0.8702 (m110) REVERT: C 122 THR cc_start: 0.9199 (p) cc_final: 0.8326 (p) REVERT: C 144 MET cc_start: 0.7498 (mmp) cc_final: 0.6643 (mmp) REVERT: C 148 LEU cc_start: 0.8931 (tp) cc_final: 0.8461 (tt) REVERT: C 293 LEU cc_start: 0.9287 (pt) cc_final: 0.8126 (mm) REVERT: C 326 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9016 (tttt) REVERT: C 330 LEU cc_start: 0.9449 (tp) cc_final: 0.8847 (tp) REVERT: C 334 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 410 MET cc_start: 0.9485 (mtm) cc_final: 0.9110 (mtp) REVERT: C 582 PHE cc_start: 0.6256 (t80) cc_final: 0.5907 (t80) REVERT: C 588 LEU cc_start: 0.9269 (tt) cc_final: 0.9030 (tt) REVERT: D 26 GLU cc_start: 0.8862 (pt0) cc_final: 0.8450 (pm20) REVERT: D 75 MET cc_start: 0.9086 (ptt) cc_final: 0.8582 (ptt) REVERT: D 107 ASP cc_start: 0.8407 (t0) cc_final: 0.7991 (t0) REVERT: D 198 ILE cc_start: 0.8827 (mm) cc_final: 0.8590 (mm) REVERT: D 259 ASP cc_start: 0.8244 (t70) cc_final: 0.7984 (t0) REVERT: D 321 LEU cc_start: 0.8617 (mt) cc_final: 0.8250 (mt) REVERT: D 339 TYR cc_start: 0.7273 (t80) cc_final: 0.6682 (t80) REVERT: D 348 MET cc_start: 0.9137 (mmm) cc_final: 0.7998 (mmm) REVERT: D 352 GLU cc_start: 0.9525 (mm-30) cc_final: 0.8891 (mm-30) REVERT: D 378 HIS cc_start: 0.9191 (t70) cc_final: 0.8898 (t70) REVERT: D 401 LEU cc_start: 0.8357 (tp) cc_final: 0.8069 (tp) REVERT: E 34 PHE cc_start: 0.9349 (t80) cc_final: 0.8856 (t80) REVERT: E 126 LYS cc_start: 0.7924 (tmtt) cc_final: 0.7554 (tptt) REVERT: E 128 GLU cc_start: 0.9200 (pm20) cc_final: 0.8802 (pm20) REVERT: E 132 ASP cc_start: 0.9431 (m-30) cc_final: 0.9061 (p0) REVERT: E 188 GLN cc_start: 0.7956 (mt0) cc_final: 0.7646 (mt0) REVERT: E 191 LEU cc_start: 0.9099 (tp) cc_final: 0.8720 (tp) REVERT: E 314 TYR cc_start: 0.7836 (t80) cc_final: 0.7388 (t80) REVERT: E 351 LEU cc_start: 0.9026 (mt) cc_final: 0.8283 (pp) REVERT: E 379 ASN cc_start: 0.9421 (t0) cc_final: 0.9133 (t0) REVERT: E 383 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8621 (pp30) REVERT: E 384 ILE cc_start: 0.9085 (tt) cc_final: 0.8868 (tt) REVERT: E 416 ILE cc_start: 0.8932 (mm) cc_final: 0.8719 (mm) outliers start: 1 outliers final: 1 residues processed: 400 average time/residue: 0.2360 time to fit residues: 142.5751 Evaluate side-chains 313 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 0.0030 chunk 124 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 106 optimal weight: 0.0980 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN B 372 GLN B 393 HIS ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 HIS D 166 HIS D 225 GLN ** D 351 ASN ** 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 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.7708 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= 0.169 Angle : 0.705 11.767 20038 Z= 0.355 Chirality : 0.044 0.201 2295 Planarity : 0.005 0.112 2525 Dihedral : 7.387 88.799 1964 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.12 % Allowed : 1.72 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1733 helix: 0.12 (0.16), residues: 1001 sheet: -1.38 (0.48), residues: 112 loop : -1.91 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 301 HIS 0.010 0.001 HIS E 27 PHE 0.028 0.002 PHE B 492 TYR 0.024 0.001 TYR E 304 ARG 0.007 0.000 ARG E 104 *********************** 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 405 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 403 time to evaluate : 1.764 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: A 795 PHE cc_start: 0.8773 (t80) cc_final: 0.7868 (t80) REVERT: A 799 TYR cc_start: 0.9440 (t80) cc_final: 0.8989 (t80) REVERT: A 816 MET cc_start: 0.9294 (ptt) cc_final: 0.8859 (pmm) REVERT: A 825 HIS cc_start: 0.9451 (m90) cc_final: 0.9233 (m90) REVERT: A 826 LEU cc_start: 0.9229 (mt) cc_final: 0.8925 (mt) REVERT: A 843 LEU cc_start: 0.8435 (tp) cc_final: 0.7981 (tp) REVERT: B 302 MET cc_start: 0.8986 (ppp) cc_final: 0.8663 (ppp) REVERT: B 303 LEU cc_start: 0.8877 (tp) cc_final: 0.8517 (mt) REVERT: B 325 ARG cc_start: 0.9007 (ptm160) cc_final: 0.8653 (ptt180) REVERT: B 330 MET cc_start: 0.8082 (mtm) cc_final: 0.7449 (mmm) REVERT: B 394 ASN cc_start: 0.8737 (t0) cc_final: 0.8525 (t0) REVERT: B 395 LEU cc_start: 0.8438 (tp) cc_final: 0.8173 (tt) REVERT: B 403 GLU cc_start: 0.8583 (mp0) cc_final: 0.8376 (mp0) REVERT: B 426 HIS cc_start: 0.8200 (t-90) cc_final: 0.7829 (t70) REVERT: B 432 MET cc_start: 0.8273 (ptt) cc_final: 0.7709 (ptm) REVERT: B 493 ARG cc_start: 0.7067 (tpm170) cc_final: 0.6673 (tpm170) REVERT: B 532 LEU cc_start: 0.9250 (tp) cc_final: 0.8802 (tt) REVERT: B 536 LEU cc_start: 0.9032 (mt) cc_final: 0.8694 (pp) REVERT: C 50 ILE cc_start: 0.9636 (mt) cc_final: 0.9415 (tp) REVERT: C 66 ASN cc_start: 0.9532 (m-40) cc_final: 0.8749 (m110) REVERT: C 77 LEU cc_start: 0.9434 (mm) cc_final: 0.9128 (pp) REVERT: C 122 THR cc_start: 0.9158 (p) cc_final: 0.8271 (p) REVERT: C 148 LEU cc_start: 0.9058 (tp) cc_final: 0.8604 (tt) REVERT: C 221 ASP cc_start: 0.8103 (t0) cc_final: 0.7622 (t0) REVERT: C 293 LEU cc_start: 0.9206 (pt) cc_final: 0.8065 (mm) REVERT: C 326 LYS cc_start: 0.9385 (ttpt) cc_final: 0.8960 (tttt) REVERT: C 330 LEU cc_start: 0.9446 (tp) cc_final: 0.9189 (tp) REVERT: C 410 MET cc_start: 0.9437 (mtm) cc_final: 0.9052 (mtt) REVERT: C 412 TYR cc_start: 0.7684 (t80) cc_final: 0.7471 (t80) REVERT: C 582 PHE cc_start: 0.6368 (t80) cc_final: 0.6155 (t80) REVERT: D 26 GLU cc_start: 0.8847 (pt0) cc_final: 0.8341 (pm20) REVERT: D 44 TYR cc_start: 0.8371 (t80) cc_final: 0.8147 (t80) REVERT: D 75 MET cc_start: 0.9077 (ptt) cc_final: 0.8405 (ptt) REVERT: D 169 ASN cc_start: 0.8380 (t0) cc_final: 0.7967 (p0) REVERT: D 198 ILE cc_start: 0.8720 (mm) cc_final: 0.8424 (mm) REVERT: D 221 PHE cc_start: 0.8746 (p90) cc_final: 0.8454 (p90) REVERT: D 225 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8417 (tp-100) REVERT: D 269 HIS cc_start: 0.8995 (m-70) cc_final: 0.8502 (m-70) REVERT: D 278 SER cc_start: 0.8948 (t) cc_final: 0.7596 (t) REVERT: D 312 ASP cc_start: 0.7907 (p0) cc_final: 0.7664 (p0) REVERT: D 321 LEU cc_start: 0.8560 (mt) cc_final: 0.8247 (mt) REVERT: D 339 TYR cc_start: 0.7323 (t80) cc_final: 0.7018 (t80) REVERT: D 348 MET cc_start: 0.9128 (mmm) cc_final: 0.8067 (mmm) REVERT: D 376 PHE cc_start: 0.8623 (t80) cc_final: 0.8406 (t80) REVERT: E 34 PHE cc_start: 0.9390 (t80) cc_final: 0.8917 (t80) REVERT: E 132 ASP cc_start: 0.9458 (m-30) cc_final: 0.9078 (p0) REVERT: E 188 GLN cc_start: 0.7929 (mt0) cc_final: 0.7699 (mt0) REVERT: E 318 TYR cc_start: 0.8766 (m-10) cc_final: 0.8437 (m-10) REVERT: E 351 LEU cc_start: 0.8981 (mt) cc_final: 0.8250 (pp) REVERT: E 379 ASN cc_start: 0.9304 (t0) cc_final: 0.9038 (t0) REVERT: E 383 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8539 (pp30) REVERT: E 415 PHE cc_start: 0.8937 (t80) cc_final: 0.8614 (t80) outliers start: 2 outliers final: 1 residues processed: 405 average time/residue: 0.2401 time to fit residues: 146.8154 Evaluate side-chains 330 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 328 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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: 7.9990 chunk 101 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 115 optimal weight: 0.0970 chunk 83 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS ** D 351 ASN ** 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 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.7931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14804 Z= 0.174 Angle : 0.725 12.959 20038 Z= 0.362 Chirality : 0.044 0.190 2295 Planarity : 0.005 0.105 2525 Dihedral : 7.222 85.849 1964 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.12 % Allowed : 1.47 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1733 helix: 0.05 (0.16), residues: 1002 sheet: -1.45 (0.48), residues: 112 loop : -1.92 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 301 HIS 0.006 0.001 HIS E 27 PHE 0.027 0.002 PHE B 492 TYR 0.022 0.001 TYR E 304 ARG 0.008 0.000 ARG A 830 *********************** 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 401 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 1.773 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 799 TYR cc_start: 0.9472 (t80) cc_final: 0.9121 (t80) REVERT: A 825 HIS cc_start: 0.9439 (m90) cc_final: 0.9227 (m90) REVERT: A 826 LEU cc_start: 0.9197 (mt) cc_final: 0.8946 (mt) REVERT: B 302 MET cc_start: 0.8946 (ppp) cc_final: 0.8658 (ppp) REVERT: B 303 LEU cc_start: 0.8869 (tp) cc_final: 0.8504 (mt) REVERT: B 395 LEU cc_start: 0.8407 (tp) cc_final: 0.8004 (tt) REVERT: B 403 GLU cc_start: 0.8508 (mp0) cc_final: 0.8257 (mp0) REVERT: B 432 MET cc_start: 0.8238 (ptt) cc_final: 0.7834 (ptm) REVERT: B 493 ARG cc_start: 0.7080 (tpm170) cc_final: 0.6836 (tpm170) REVERT: B 532 LEU cc_start: 0.9250 (tp) cc_final: 0.8854 (tt) REVERT: B 536 LEU cc_start: 0.8996 (mt) cc_final: 0.8724 (pp) REVERT: C 50 ILE cc_start: 0.9632 (mt) cc_final: 0.9416 (tp) REVERT: C 66 ASN cc_start: 0.9498 (m-40) cc_final: 0.8862 (m110) REVERT: C 77 LEU cc_start: 0.9427 (mm) cc_final: 0.9139 (pp) REVERT: C 148 LEU cc_start: 0.8981 (tp) cc_final: 0.8474 (tt) REVERT: C 221 ASP cc_start: 0.8281 (t0) cc_final: 0.7555 (t0) REVERT: C 293 LEU cc_start: 0.9207 (pt) cc_final: 0.8070 (mm) REVERT: C 316 TYR cc_start: 0.8038 (m-80) cc_final: 0.7681 (m-80) REVERT: C 326 LYS cc_start: 0.9407 (ttpt) cc_final: 0.8795 (tttp) REVERT: C 330 LEU cc_start: 0.9360 (tp) cc_final: 0.8993 (tp) REVERT: C 334 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8130 (mt-10) REVERT: C 410 MET cc_start: 0.9437 (mtm) cc_final: 0.9103 (mtt) REVERT: C 582 PHE cc_start: 0.6481 (t80) cc_final: 0.6107 (t80) REVERT: C 694 ILE cc_start: 0.8557 (mm) cc_final: 0.8324 (mm) REVERT: D 26 GLU cc_start: 0.8874 (pt0) cc_final: 0.8356 (pm20) REVERT: D 75 MET cc_start: 0.8989 (ptt) cc_final: 0.8336 (ptt) REVERT: D 81 LEU cc_start: 0.9381 (mm) cc_final: 0.9074 (pp) REVERT: D 169 ASN cc_start: 0.8594 (t0) cc_final: 0.8273 (p0) REVERT: D 194 CYS cc_start: 0.7121 (t) cc_final: 0.5656 (t) REVERT: D 198 ILE cc_start: 0.8799 (mm) cc_final: 0.8556 (mm) REVERT: D 200 GLU cc_start: 0.9230 (pm20) cc_final: 0.8962 (pm20) REVERT: D 259 ASP cc_start: 0.8527 (t70) cc_final: 0.8252 (t0) REVERT: D 269 HIS cc_start: 0.8984 (m-70) cc_final: 0.8506 (m-70) REVERT: D 278 SER cc_start: 0.8957 (t) cc_final: 0.7633 (t) REVERT: D 312 ASP cc_start: 0.7928 (p0) cc_final: 0.7702 (p0) REVERT: D 321 LEU cc_start: 0.8589 (mt) cc_final: 0.8182 (mt) REVERT: D 339 TYR cc_start: 0.7714 (t80) cc_final: 0.7432 (t80) REVERT: D 348 MET cc_start: 0.9201 (mmm) cc_final: 0.8205 (mpp) REVERT: D 352 GLU cc_start: 0.9409 (mm-30) cc_final: 0.8851 (mm-30) REVERT: D 378 HIS cc_start: 0.9281 (t70) cc_final: 0.9019 (t70) REVERT: D 401 LEU cc_start: 0.8349 (tp) cc_final: 0.8108 (tp) REVERT: D 428 TRP cc_start: 0.7298 (t-100) cc_final: 0.6098 (t-100) REVERT: E 34 PHE cc_start: 0.9213 (t80) cc_final: 0.8767 (t80) REVERT: E 105 LEU cc_start: 0.8144 (mt) cc_final: 0.7804 (mt) REVERT: E 142 LEU cc_start: 0.8977 (mt) cc_final: 0.8768 (mt) REVERT: E 318 TYR cc_start: 0.8790 (m-10) cc_final: 0.8555 (m-10) REVERT: E 351 LEU cc_start: 0.8980 (mt) cc_final: 0.8562 (pp) REVERT: E 379 ASN cc_start: 0.9258 (t0) cc_final: 0.8987 (t0) REVERT: E 415 PHE cc_start: 0.8933 (t80) cc_final: 0.8687 (t80) outliers start: 2 outliers final: 1 residues processed: 401 average time/residue: 0.2325 time to fit residues: 141.1396 Evaluate side-chains 321 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 0.0030 chunk 68 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS B 393 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** 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 82 HIS E 227 HIS E 266 GLN E 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.8179 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= 0.178 Angle : 0.739 12.301 20038 Z= 0.371 Chirality : 0.045 0.182 2295 Planarity : 0.005 0.097 2525 Dihedral : 7.168 86.476 1964 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.12 % Allowed : 0.68 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1733 helix: 0.08 (0.16), residues: 995 sheet: -1.27 (0.50), residues: 103 loop : -1.95 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 301 HIS 0.010 0.001 HIS C 678 PHE 0.027 0.002 PHE B 492 TYR 0.022 0.001 TYR E 304 ARG 0.009 0.001 ARG D 69 *********************** 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 389 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 1.693 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 825 HIS cc_start: 0.9449 (m90) cc_final: 0.9244 (m90) REVERT: A 826 LEU cc_start: 0.9200 (mt) cc_final: 0.8994 (mt) REVERT: B 302 MET cc_start: 0.9040 (ppp) cc_final: 0.8508 (ppp) REVERT: B 303 LEU cc_start: 0.8785 (tp) cc_final: 0.8438 (mt) REVERT: B 395 LEU cc_start: 0.8395 (tp) cc_final: 0.8154 (tt) REVERT: B 403 GLU cc_start: 0.8405 (mp0) cc_final: 0.8191 (mp0) REVERT: B 432 MET cc_start: 0.8047 (ptt) cc_final: 0.7694 (ptm) REVERT: B 493 ARG cc_start: 0.7098 (tpm170) cc_final: 0.6834 (tpm170) REVERT: B 532 LEU cc_start: 0.9265 (tp) cc_final: 0.8839 (tt) REVERT: B 536 LEU cc_start: 0.9005 (mt) cc_final: 0.8717 (pp) REVERT: C 77 LEU cc_start: 0.9435 (mm) cc_final: 0.9131 (pp) REVERT: C 123 GLU cc_start: 0.8804 (pm20) cc_final: 0.8550 (pm20) REVERT: C 148 LEU cc_start: 0.8965 (tp) cc_final: 0.8489 (tt) REVERT: C 221 ASP cc_start: 0.8364 (t0) cc_final: 0.7678 (t0) REVERT: C 289 LEU cc_start: 0.9399 (tt) cc_final: 0.8912 (pp) REVERT: C 293 LEU cc_start: 0.9193 (pt) cc_final: 0.7923 (mm) REVERT: C 326 LYS cc_start: 0.9453 (ttpt) cc_final: 0.8914 (tttp) REVERT: C 330 LEU cc_start: 0.9341 (tp) cc_final: 0.8987 (tp) REVERT: C 334 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8155 (mt-10) REVERT: C 409 HIS cc_start: 0.9365 (m90) cc_final: 0.9075 (m90) REVERT: C 410 MET cc_start: 0.9433 (mtm) cc_final: 0.9140 (mtt) REVERT: C 582 PHE cc_start: 0.6477 (t80) cc_final: 0.6109 (t80) REVERT: C 588 LEU cc_start: 0.9247 (tt) cc_final: 0.9043 (tt) REVERT: C 693 PHE cc_start: 0.8256 (m-80) cc_final: 0.7986 (m-80) REVERT: D 75 MET cc_start: 0.8889 (ptt) cc_final: 0.8307 (ptt) REVERT: D 81 LEU cc_start: 0.9442 (mm) cc_final: 0.8990 (pp) REVERT: D 169 ASN cc_start: 0.8219 (t0) cc_final: 0.7887 (p0) REVERT: D 198 ILE cc_start: 0.9044 (mm) cc_final: 0.8819 (mm) REVERT: D 200 GLU cc_start: 0.9211 (pm20) cc_final: 0.8933 (pm20) REVERT: D 259 ASP cc_start: 0.8596 (t70) cc_final: 0.8305 (t0) REVERT: D 269 HIS cc_start: 0.8977 (m-70) cc_final: 0.8495 (m-70) REVERT: D 275 ASN cc_start: 0.9277 (p0) cc_final: 0.8692 (p0) REVERT: D 278 SER cc_start: 0.8984 (t) cc_final: 0.7694 (t) REVERT: D 312 ASP cc_start: 0.7952 (p0) cc_final: 0.7694 (p0) REVERT: D 321 LEU cc_start: 0.8670 (mt) cc_final: 0.8217 (mt) REVERT: D 339 TYR cc_start: 0.7859 (t80) cc_final: 0.7625 (t80) REVERT: D 348 MET cc_start: 0.9254 (mmm) cc_final: 0.8387 (mmm) REVERT: D 378 HIS cc_start: 0.9284 (t70) cc_final: 0.8965 (t70) REVERT: D 428 TRP cc_start: 0.7369 (t-100) cc_final: 0.6172 (t-100) REVERT: E 34 PHE cc_start: 0.9226 (t80) cc_final: 0.8840 (t80) REVERT: E 105 LEU cc_start: 0.8135 (mt) cc_final: 0.7688 (mt) REVERT: E 141 PHE cc_start: 0.8452 (m-80) cc_final: 0.8206 (m-80) REVERT: E 164 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8298 (tmtt) REVERT: E 191 LEU cc_start: 0.9175 (mm) cc_final: 0.8897 (mm) REVERT: E 238 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8407 (tm-30) REVERT: E 314 TYR cc_start: 0.7599 (t80) cc_final: 0.7248 (t80) REVERT: E 351 LEU cc_start: 0.8945 (mt) cc_final: 0.8429 (pp) REVERT: E 379 ASN cc_start: 0.9298 (t0) cc_final: 0.9021 (t0) REVERT: E 383 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8306 (pp30) REVERT: E 384 ILE cc_start: 0.9008 (tt) cc_final: 0.8770 (tt) REVERT: E 415 PHE cc_start: 0.8949 (t80) cc_final: 0.8723 (t80) REVERT: E 416 ILE cc_start: 0.8915 (mm) cc_final: 0.8554 (mm) outliers start: 2 outliers final: 1 residues processed: 389 average time/residue: 0.2429 time to fit residues: 142.5339 Evaluate side-chains 318 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 316 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 HIS C 146 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** 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 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.8401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14804 Z= 0.230 Angle : 0.765 11.731 20038 Z= 0.390 Chirality : 0.046 0.176 2295 Planarity : 0.005 0.093 2525 Dihedral : 7.466 83.756 1964 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.06 % Allowed : 0.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1733 helix: 0.03 (0.16), residues: 993 sheet: -0.97 (0.46), residues: 117 loop : -1.97 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP B 301 HIS 0.011 0.001 HIS B 299 PHE 0.029 0.002 PHE B 539 TYR 0.022 0.002 TYR C 47 ARG 0.007 0.001 ARG E 104 ********************** 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 368 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 367 time to evaluate : 1.622 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: A 795 PHE cc_start: 0.8844 (t80) cc_final: 0.7964 (t80) REVERT: A 799 TYR cc_start: 0.9530 (t80) cc_final: 0.9277 (t80) REVERT: A 807 ARG cc_start: 0.9423 (pmt-80) cc_final: 0.9192 (pmt-80) REVERT: A 825 HIS cc_start: 0.9501 (m90) cc_final: 0.9300 (m90) REVERT: A 826 LEU cc_start: 0.9200 (mt) cc_final: 0.8918 (mt) REVERT: B 302 MET cc_start: 0.8751 (ppp) cc_final: 0.8471 (ppp) REVERT: B 303 LEU cc_start: 0.9006 (tp) cc_final: 0.8698 (mt) REVERT: B 394 ASN cc_start: 0.8789 (t0) cc_final: 0.8575 (t0) REVERT: B 395 LEU cc_start: 0.8627 (tp) cc_final: 0.8392 (tt) REVERT: B 426 HIS cc_start: 0.8782 (t-90) cc_final: 0.8557 (t-90) REVERT: B 432 MET cc_start: 0.8096 (ptt) cc_final: 0.7732 (ptm) REVERT: B 493 ARG cc_start: 0.7120 (tpm170) cc_final: 0.6896 (tpm170) REVERT: B 532 LEU cc_start: 0.9284 (tp) cc_final: 0.8911 (tt) REVERT: B 536 LEU cc_start: 0.9040 (mt) cc_final: 0.8716 (pp) REVERT: C 77 LEU cc_start: 0.9459 (mm) cc_final: 0.9120 (pp) REVERT: C 123 GLU cc_start: 0.8909 (pm20) cc_final: 0.8606 (pm20) REVERT: C 143 ASP cc_start: 0.8095 (p0) cc_final: 0.7492 (p0) REVERT: C 146 HIS cc_start: 0.7897 (m170) cc_final: 0.7649 (m90) REVERT: C 148 LEU cc_start: 0.9007 (tp) cc_final: 0.8499 (tt) REVERT: C 221 ASP cc_start: 0.8462 (t0) cc_final: 0.7879 (t0) REVERT: C 289 LEU cc_start: 0.9456 (tt) cc_final: 0.8930 (pp) REVERT: C 293 LEU cc_start: 0.9252 (pt) cc_final: 0.7984 (mm) REVERT: C 318 ASP cc_start: 0.8757 (p0) cc_final: 0.8510 (p0) REVERT: C 409 HIS cc_start: 0.9383 (m90) cc_final: 0.9117 (m90) REVERT: C 410 MET cc_start: 0.9481 (mtm) cc_final: 0.9156 (mtt) REVERT: C 440 CYS cc_start: 0.9298 (t) cc_final: 0.8974 (m) REVERT: C 582 PHE cc_start: 0.6565 (t80) cc_final: 0.6190 (t80) REVERT: C 693 PHE cc_start: 0.8310 (m-80) cc_final: 0.8106 (m-80) REVERT: D 75 MET cc_start: 0.8949 (ptt) cc_final: 0.8438 (ptt) REVERT: D 81 LEU cc_start: 0.9459 (mm) cc_final: 0.8980 (pp) REVERT: D 169 ASN cc_start: 0.8438 (t0) cc_final: 0.8201 (t0) REVERT: D 198 ILE cc_start: 0.9003 (mm) cc_final: 0.8738 (mm) REVERT: D 269 HIS cc_start: 0.9085 (m-70) cc_final: 0.8620 (m-70) REVERT: D 312 ASP cc_start: 0.8079 (p0) cc_final: 0.7788 (p0) REVERT: D 321 LEU cc_start: 0.8732 (mt) cc_final: 0.8288 (mt) REVERT: D 339 TYR cc_start: 0.7817 (t80) cc_final: 0.7359 (t80) REVERT: D 348 MET cc_start: 0.9296 (mmm) cc_final: 0.8440 (mmm) REVERT: D 378 HIS cc_start: 0.9363 (t70) cc_final: 0.8988 (t70) REVERT: D 401 LEU cc_start: 0.8387 (tp) cc_final: 0.8146 (tp) REVERT: E 34 PHE cc_start: 0.9301 (t80) cc_final: 0.8858 (t80) REVERT: E 105 LEU cc_start: 0.8183 (mt) cc_final: 0.7763 (mt) REVERT: E 126 LYS cc_start: 0.7924 (tmtt) cc_final: 0.7691 (tptp) REVERT: E 129 TYR cc_start: 0.7780 (m-80) cc_final: 0.7510 (m-80) REVERT: E 132 ASP cc_start: 0.9523 (m-30) cc_final: 0.9224 (p0) REVERT: E 141 PHE cc_start: 0.8311 (m-80) cc_final: 0.7988 (m-80) REVERT: E 163 GLU cc_start: 0.8881 (mp0) cc_final: 0.8527 (pm20) REVERT: E 164 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8360 (tmtt) REVERT: E 238 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8525 (tm-30) REVERT: E 314 TYR cc_start: 0.8005 (t80) cc_final: 0.7648 (t80) REVERT: E 351 LEU cc_start: 0.9015 (mt) cc_final: 0.8521 (pp) REVERT: E 379 ASN cc_start: 0.9502 (t0) cc_final: 0.9184 (t0) REVERT: E 383 GLN cc_start: 0.8753 (pp30) cc_final: 0.8247 (pp30) REVERT: E 415 PHE cc_start: 0.8982 (t80) cc_final: 0.8777 (t80) REVERT: E 416 ILE cc_start: 0.8953 (mm) cc_final: 0.8572 (mm) outliers start: 1 outliers final: 1 residues processed: 368 average time/residue: 0.2425 time to fit residues: 134.7980 Evaluate side-chains 295 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.070255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053510 restraints weight = 71232.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055042 restraints weight = 50704.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056122 restraints weight = 39554.245| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.8545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14804 Z= 0.186 Angle : 0.754 12.184 20038 Z= 0.378 Chirality : 0.045 0.187 2295 Planarity : 0.005 0.096 2525 Dihedral : 7.308 83.664 1964 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.06 % Allowed : 0.80 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1733 helix: 0.09 (0.16), residues: 994 sheet: -0.97 (0.45), residues: 118 loop : -1.94 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP B 301 HIS 0.007 0.001 HIS E 27 PHE 0.028 0.002 PHE C 319 TYR 0.018 0.001 TYR E 304 ARG 0.006 0.001 ARG E 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.65 seconds wall clock time: 65 minutes 3.04 seconds (3903.04 seconds total)