Starting phenix.real_space_refine on Wed Jan 14 19:16:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m2z_23638/01_2026/7m2z_23638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m2z_23638/01_2026/7m2z_23638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m2z_23638/01_2026/7m2z_23638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m2z_23638/01_2026/7m2z_23638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m2z_23638/01_2026/7m2z_23638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m2z_23638/01_2026/7m2z_23638.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.195 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 4 5.49 5 S 78 5.16 5 C 11669 2.51 5 N 3078 2.21 5 O 3501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18330 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3486 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 1 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 5569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5569 Classifications: {'peptide': 674} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 654} Chain breaks: 1 Chain: "D" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5778 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 24, 'TRANS': 668} Chain breaks: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.77, per 1000 atoms: 0.21 Number of scatterers: 18330 At special positions: 0 Unit cell: (133.487, 115.939, 185.503, 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 78 16.00 P 4 15.00 O 3501 8.00 N 3078 7.00 C 11669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 759.1 milliseconds 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4316 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 13 sheets defined 60.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 72 through 83 removed outlier: 4.608A pdb=" N ILE B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 103 through 128 removed outlier: 4.049A pdb=" N ASN B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASP B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASP B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.656A pdb=" N SER B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.641A pdb=" N ILE B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 228 through 238 removed outlier: 3.996A pdb=" N SER B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.759A pdb=" N ILE B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.713A pdb=" N ILE B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 393 through 399 removed outlier: 3.542A pdb=" N VAL B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 442 removed outlier: 3.506A pdb=" N VAL B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 441 " --> pdb=" O TYR B 437 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 451 removed outlier: 3.702A pdb=" N VAL B 451 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 29 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.558A pdb=" N ASP A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 104 through 128 removed outlier: 4.408A pdb=" N GLY A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASP A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 162 Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.421A pdb=" N LEU A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.535A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.517A pdb=" N ILE A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 299 through 304 removed outlier: 5.914A pdb=" N SER A 302 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.696A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 removed outlier: 4.086A pdb=" N PHE A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 397 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.889A pdb=" N TYR A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 442 removed outlier: 3.552A pdb=" N VAL A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.681A pdb=" N TYR C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 removed outlier: 4.627A pdb=" N ALA C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 275 Processing helix chain 'C' and resid 279 through 301 removed outlier: 5.025A pdb=" N GLU C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASN C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 301 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.868A pdb=" N PHE C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 353 Processing helix chain 'C' and resid 387 through 390 removed outlier: 3.951A pdb=" N VAL C 390 " --> pdb=" O GLN C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 395 through 415 removed outlier: 3.586A pdb=" N TYR C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 442 through 467 Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 485 through 496 removed outlier: 4.338A pdb=" N MET C 489 " --> pdb=" O LYS C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 removed outlier: 3.642A pdb=" N ALA C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 523 removed outlier: 3.911A pdb=" N LEU C 512 " --> pdb=" O PRO C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 removed outlier: 3.935A pdb=" N SER C 531 " --> pdb=" O HIS C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 540 removed outlier: 3.759A pdb=" N ASN C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 540' Processing helix chain 'C' and resid 567 through 572 removed outlier: 3.742A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 615 removed outlier: 4.353A pdb=" N PHE C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 656 removed outlier: 3.781A pdb=" N ARG C 625 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 645 " --> pdb=" O PHE C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.689A pdb=" N ASN C 660 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 737 Processing helix chain 'C' and resid 757 through 792 removed outlier: 3.792A pdb=" N LEU C 792 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 834 removed outlier: 3.552A pdb=" N GLY C 803 " --> pdb=" O ASN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 99 through 104 removed outlier: 3.744A pdb=" N LYS D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 126 removed outlier: 3.654A pdb=" N ILE D 109 " --> pdb=" O PHE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.357A pdb=" N SER D 130 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 148 removed outlier: 3.657A pdb=" N GLN D 136 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 165 removed outlier: 3.546A pdb=" N THR D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU D 156 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 180 Processing helix chain 'D' and resid 181 through 206 removed outlier: 3.642A pdb=" N GLN D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 Processing helix chain 'D' and resid 261 through 276 removed outlier: 3.618A pdb=" N SER D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 290 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 337 through 362 removed outlier: 3.629A pdb=" N LYS D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.657A pdb=" N SER D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 371' Processing helix chain 'D' and resid 380 through 387 removed outlier: 3.554A pdb=" N LEU D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 411 Processing helix chain 'D' and resid 414 through 427 removed outlier: 3.503A pdb=" N ILE D 425 " --> pdb=" O HIS D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 450 removed outlier: 5.663A pdb=" N GLY D 444 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLU D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS D 448 " --> pdb=" O GLY D 444 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 472 removed outlier: 3.815A pdb=" N LEU D 462 " --> pdb=" O TYR D 458 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN D 470 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU D 472 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 4.031A pdb=" N GLN D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 476 through 481' Processing helix chain 'D' and resid 490 through 496 Processing helix chain 'D' and resid 570 through 574 Processing helix chain 'D' and resid 576 through 607 Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 625 through 652 removed outlier: 3.566A pdb=" N ILE D 652 " --> pdb=" O ASN D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 663 removed outlier: 3.566A pdb=" N VAL D 656 " --> pdb=" O ILE D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 685 Processing helix chain 'D' and resid 686 through 691 removed outlier: 3.757A pdb=" N SER D 690 " --> pdb=" O ASN D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 717 removed outlier: 4.484A pdb=" N ALA D 715 " --> pdb=" O LYS D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'D' and resid 757 through 789 removed outlier: 3.703A pdb=" N GLU D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 811 removed outlier: 3.815A pdb=" N SER D 810 " --> pdb=" O VAL D 807 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 6 removed outlier: 7.287A pdb=" N GLU B 4 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE B 136 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE B 6 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 166 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR B 168 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 4 through 6 removed outlier: 7.287A pdb=" N GLU B 4 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE B 136 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE B 6 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 166 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR B 168 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 200 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 267 " --> pdb=" O MET B 380 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N MET B 380 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 373 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 322 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET B 375 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN B 320 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 377 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL B 318 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B 379 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.222A pdb=" N MET B 68 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 69 removed outlier: 5.745A pdb=" N GLU A 4 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 135 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU A 134 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR A 168 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE A 136 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TYR A 170 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 138 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL A 172 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 200 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 201 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL A 203 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N PHE A 272 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 14.445A pdb=" N ASP A 205 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A 267 " --> pdb=" O MET A 380 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET A 380 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A 317 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA7, first strand: chain 'C' and resid 207 through 209 removed outlier: 4.350A pdb=" N ASP D 8 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 364 through 366 Processing sheet with id=AA9, first strand: chain 'C' and resid 541 through 544 Processing sheet with id=AB1, first strand: chain 'C' and resid 681 through 683 removed outlier: 3.569A pdb=" N GLU C 690 " --> pdb=" O ILE C 682 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB3, first strand: chain 'D' and resid 232 through 234 removed outlier: 3.549A pdb=" N ILE D 326 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D 325 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 302 " --> pdb=" O PHE D 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 483 through 486 removed outlier: 3.659A pdb=" N MET D 483 " --> pdb=" O ASP D 563 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 563 " --> pdb=" O MET D 483 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5107 1.33 - 1.45: 3202 1.45 - 1.57: 10257 1.57 - 1.69: 6 1.69 - 1.81: 137 Bond restraints: 18709 Sorted by residual: bond pdb=" C TYR B 362 " pdb=" N LEU B 363 " ideal model delta sigma weight residual 1.330 1.226 0.104 1.47e-02 4.63e+03 5.04e+01 bond pdb=" CB MET A 248 " pdb=" CG MET A 248 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 5.04e+00 bond pdb=" C GLN B 38 " pdb=" N LEU B 39 " ideal model delta sigma weight residual 1.333 1.300 0.033 1.59e-02 3.96e+03 4.27e+00 bond pdb=" CB TYR D 558 " pdb=" CG TYR D 558 " ideal model delta sigma weight residual 1.512 1.468 0.044 2.20e-02 2.07e+03 4.09e+00 bond pdb=" CB TRP B 93 " pdb=" CG TRP B 93 " ideal model delta sigma weight residual 1.498 1.437 0.061 3.10e-02 1.04e+03 3.89e+00 ... (remaining 18704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 24347 2.08 - 4.16: 874 4.16 - 6.24: 91 6.24 - 8.32: 16 8.32 - 10.40: 2 Bond angle restraints: 25330 Sorted by residual: angle pdb=" CA TYR D 558 " pdb=" CB TYR D 558 " pdb=" CG TYR D 558 " ideal model delta sigma weight residual 113.90 106.11 7.79 1.80e+00 3.09e-01 1.87e+01 angle pdb=" N GLU C 771 " pdb=" CA GLU C 771 " pdb=" CB GLU C 771 " ideal model delta sigma weight residual 110.12 115.44 -5.32 1.47e+00 4.63e-01 1.31e+01 angle pdb=" C LEU D 692 " pdb=" N ILE D 693 " pdb=" CA ILE D 693 " ideal model delta sigma weight residual 120.24 122.50 -2.26 6.30e-01 2.52e+00 1.28e+01 angle pdb=" C ILE B 255 " pdb=" N TYR B 256 " pdb=" CA TYR B 256 " ideal model delta sigma weight residual 120.72 114.83 5.89 1.67e+00 3.59e-01 1.25e+01 angle pdb=" N VAL A 409 " pdb=" CA VAL A 409 " pdb=" CB VAL A 409 " ideal model delta sigma weight residual 112.06 108.69 3.37 9.70e-01 1.06e+00 1.21e+01 ... (remaining 25325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 10639 23.61 - 47.23: 588 47.23 - 70.84: 53 70.84 - 94.45: 23 94.45 - 118.07: 2 Dihedral angle restraints: 11305 sinusoidal: 4643 harmonic: 6662 Sorted by residual: dihedral pdb=" CA PRO D 30 " pdb=" C PRO D 30 " pdb=" N LEU D 31 " pdb=" CA LEU D 31 " ideal model delta harmonic sigma weight residual 180.00 144.92 35.08 0 5.00e+00 4.00e-02 4.92e+01 dihedral pdb=" CA PRO D 569 " pdb=" C PRO D 569 " pdb=" N LEU D 570 " pdb=" CA LEU D 570 " ideal model delta harmonic sigma weight residual 180.00 146.43 33.57 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" O2B GDP A 501 " pdb=" O3A GDP A 501 " pdb=" PB GDP A 501 " pdb=" PA GDP A 501 " ideal model delta sinusoidal sigma weight residual -180.00 -61.93 -118.07 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 11302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2027 0.053 - 0.105: 670 0.105 - 0.158: 119 0.158 - 0.211: 6 0.211 - 0.263: 1 Chirality restraints: 2823 Sorted by residual: chirality pdb=" CB ILE B 356 " pdb=" CA ILE B 356 " pdb=" CG1 ILE B 356 " pdb=" CG2 ILE B 356 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASN A 219 " pdb=" N ASN A 219 " pdb=" C ASN A 219 " pdb=" CB ASN A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL C 557 " pdb=" CA VAL C 557 " pdb=" CG1 VAL C 557 " pdb=" CG2 VAL C 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 2820 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 63 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO B 64 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 568 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO D 569 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 569 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 569 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 173 " -0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO A 174 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.034 5.00e-02 4.00e+02 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 225 2.58 - 3.16: 17400 3.16 - 3.74: 27830 3.74 - 4.32: 37965 4.32 - 4.90: 59555 Nonbonded interactions: 142975 Sorted by model distance: nonbonded pdb=" O LEU C 695 " pdb=" OH TYR D 413 " model vdw 2.006 3.040 nonbonded pdb=" O LEU A 224 " pdb=" OG1 THR A 227 " model vdw 2.049 3.040 nonbonded pdb=" OH TYR C 433 " pdb=" OE1 GLN C 452 " model vdw 2.059 3.040 nonbonded pdb=" O ALA A 390 " pdb=" OG1 THR A 393 " model vdw 2.118 3.040 nonbonded pdb=" OH TYR C 345 " pdb=" O ALA C 357 " model vdw 2.125 3.040 ... (remaining 142970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 278 or resid 286 through 501)) selection = (chain 'B' and (resid 3 through 446 or resid 501)) } 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=1.00 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: 17.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 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 : 0.007 0.104 18709 Z= 0.316 Angle : 0.902 10.396 25330 Z= 0.525 Chirality : 0.051 0.263 2823 Planarity : 0.005 0.072 3258 Dihedral : 14.278 118.067 6989 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.72 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2229 helix: -0.14 (0.14), residues: 1173 sheet: -0.71 (0.41), residues: 157 loop : -1.96 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 615 TYR 0.036 0.003 TYR D 594 PHE 0.026 0.003 PHE C 772 TRP 0.027 0.003 TRP B 105 HIS 0.015 0.002 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00662 (18709) covalent geometry : angle 0.90192 (25330) hydrogen bonds : bond 0.16994 ( 981) hydrogen bonds : angle 6.95971 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.663 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: B 120 LEU cc_start: 0.8549 (mt) cc_final: 0.8296 (tp) REVERT: B 248 MET cc_start: 0.5730 (mtp) cc_final: 0.4008 (mtt) REVERT: B 293 ASP cc_start: 0.8583 (m-30) cc_final: 0.8283 (t0) REVERT: B 297 ASP cc_start: 0.8122 (m-30) cc_final: 0.7584 (m-30) REVERT: B 416 MET cc_start: 0.8243 (mmm) cc_final: 0.7703 (mmp) REVERT: A 205 ASP cc_start: 0.7684 (t0) cc_final: 0.7423 (t0) REVERT: A 408 ASN cc_start: 0.7576 (m-40) cc_final: 0.7242 (t0) REVERT: C 668 LEU cc_start: 0.8211 (tt) cc_final: 0.7939 (tt) REVERT: D 659 LEU cc_start: 0.8827 (tp) cc_final: 0.8408 (tp) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.1287 time to fit residues: 87.8553 Evaluate side-chains 247 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN B 115 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 303 ASN B 370 ASN B 385 ASN ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 186 ASN A 226 HIS A 228 ASN A 229 GLN A 289 HIS A 355 ASN A 370 ASN C 169 GLN C 208 GLN C 245 ASN C 317 ASN C 380 HIS C 452 GLN C 461 ASN C 530 ASN C 550 HIS C 642 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN C 767 ASN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 433 HIS D 449 HIS ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN D 619 HIS ** D 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037122 restraints weight = 111113.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.038520 restraints weight = 73058.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039547 restraints weight = 53956.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.040327 restraints weight = 42933.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040910 restraints weight = 35870.891| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18709 Z= 0.152 Angle : 0.755 10.446 25330 Z= 0.382 Chirality : 0.047 0.236 2823 Planarity : 0.005 0.076 3258 Dihedral : 6.342 104.464 2478 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.18 % Allowed : 10.80 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2229 helix: 0.75 (0.15), residues: 1203 sheet: -0.21 (0.41), residues: 155 loop : -1.55 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 111 TYR 0.036 0.002 TYR A 256 PHE 0.027 0.002 PHE D 700 TRP 0.018 0.002 TRP B 22 HIS 0.006 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00316 (18709) covalent geometry : angle 0.75510 (25330) hydrogen bonds : bond 0.05609 ( 981) hydrogen bonds : angle 5.15311 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 0.678 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: B 115 ASN cc_start: 0.9166 (m-40) cc_final: 0.8867 (p0) REVERT: B 120 LEU cc_start: 0.9413 (mt) cc_final: 0.8982 (tt) REVERT: B 124 ASP cc_start: 0.9129 (m-30) cc_final: 0.8900 (m-30) REVERT: B 137 GLN cc_start: 0.9468 (mt0) cc_final: 0.8823 (mm-40) REVERT: B 170 TYR cc_start: 0.9538 (m-80) cc_final: 0.8812 (m-80) REVERT: B 197 ASP cc_start: 0.7702 (m-30) cc_final: 0.7148 (m-30) REVERT: B 289 HIS cc_start: 0.8843 (m90) cc_final: 0.8257 (m90) REVERT: B 293 ASP cc_start: 0.9448 (m-30) cc_final: 0.9001 (t0) REVERT: B 297 ASP cc_start: 0.9524 (m-30) cc_final: 0.9098 (m-30) REVERT: B 416 MET cc_start: 0.9242 (mmm) cc_final: 0.8908 (mmp) REVERT: B 434 MET cc_start: 0.9442 (mpp) cc_final: 0.9117 (mpp) REVERT: A 28 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9197 (mm-30) REVERT: A 83 PHE cc_start: 0.9242 (m-80) cc_final: 0.8681 (t80) REVERT: A 252 MET cc_start: 0.9433 (tpt) cc_final: 0.8856 (tpt) REVERT: A 355 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8268 (t160) REVERT: A 380 MET cc_start: 0.7504 (mmm) cc_final: 0.6972 (mmm) REVERT: A 388 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8761 (tp30) REVERT: A 408 ASN cc_start: 0.8345 (m-40) cc_final: 0.7486 (t0) REVERT: A 416 MET cc_start: 0.9357 (ppp) cc_final: 0.9116 (tmm) REVERT: C 220 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9443 (mm) REVERT: C 298 CYS cc_start: 0.9753 (OUTLIER) cc_final: 0.9364 (p) REVERT: C 338 MET cc_start: 0.8910 (mtt) cc_final: 0.8411 (mtt) REVERT: C 380 HIS cc_start: 0.9376 (OUTLIER) cc_final: 0.9002 (t-90) REVERT: C 464 LEU cc_start: 0.9499 (mt) cc_final: 0.9208 (pp) REVERT: C 490 ASP cc_start: 0.9395 (m-30) cc_final: 0.8877 (m-30) REVERT: C 603 GLU cc_start: 0.8781 (tp30) cc_final: 0.8511 (tp30) REVERT: C 646 SER cc_start: 0.9677 (m) cc_final: 0.9250 (p) REVERT: C 649 GLU cc_start: 0.9488 (tt0) cc_final: 0.9178 (pp20) REVERT: C 664 MET cc_start: 0.9649 (tmm) cc_final: 0.9437 (tmm) REVERT: C 732 LEU cc_start: 0.9729 (mt) cc_final: 0.9488 (pp) REVERT: C 786 ILE cc_start: 0.9614 (tp) cc_final: 0.9144 (pt) REVERT: D 123 TYR cc_start: 0.8997 (t80) cc_final: 0.7958 (t80) REVERT: D 126 TRP cc_start: 0.9331 (m-10) cc_final: 0.9030 (m-10) REVERT: D 143 ARG cc_start: 0.9557 (ttm170) cc_final: 0.9158 (ttm110) REVERT: D 300 MET cc_start: 0.9430 (mmp) cc_final: 0.8785 (mmp) REVERT: D 579 MET cc_start: 0.9371 (mmm) cc_final: 0.9080 (mmm) REVERT: D 597 ARG cc_start: 0.9709 (tpp80) cc_final: 0.9443 (tpt-90) REVERT: D 644 MET cc_start: 0.9359 (mtt) cc_final: 0.9131 (mmt) REVERT: D 645 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8885 (mt-10) REVERT: D 648 ASN cc_start: 0.9613 (m-40) cc_final: 0.9227 (p0) REVERT: D 700 PHE cc_start: 0.9538 (m-80) cc_final: 0.9295 (m-80) REVERT: D 713 MET cc_start: 0.9233 (mmm) cc_final: 0.8837 (mmm) REVERT: D 810 SER cc_start: 0.9548 (t) cc_final: 0.9321 (p) outliers start: 45 outliers final: 19 residues processed: 349 average time/residue: 0.1202 time to fit residues: 67.4342 Evaluate side-chains 294 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 28 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 158 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 366 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN C 469 HIS C 642 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 778 ASN C 780 ASN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.046182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.034514 restraints weight = 119919.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035837 restraints weight = 78482.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.036797 restraints weight = 58009.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037530 restraints weight = 46317.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.038098 restraints weight = 38733.230| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18709 Z= 0.231 Angle : 0.729 11.873 25330 Z= 0.381 Chirality : 0.045 0.248 2823 Planarity : 0.005 0.072 3258 Dihedral : 6.131 102.201 2478 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.57 % Allowed : 14.92 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2229 helix: 0.60 (0.14), residues: 1207 sheet: -0.40 (0.38), residues: 169 loop : -1.51 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 262 TYR 0.024 0.002 TYR D 558 PHE 0.019 0.002 PHE C 772 TRP 0.023 0.002 TRP A 105 HIS 0.016 0.002 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00457 (18709) covalent geometry : angle 0.72943 (25330) hydrogen bonds : bond 0.05227 ( 981) hydrogen bonds : angle 5.24073 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 0.745 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: B 120 LEU cc_start: 0.9433 (mt) cc_final: 0.8955 (tt) REVERT: B 124 ASP cc_start: 0.9224 (m-30) cc_final: 0.8970 (m-30) REVERT: B 289 HIS cc_start: 0.8994 (m90) cc_final: 0.8384 (m-70) REVERT: B 293 ASP cc_start: 0.9502 (m-30) cc_final: 0.9153 (t0) REVERT: B 366 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8218 (pp30) REVERT: B 380 MET cc_start: 0.8872 (ttp) cc_final: 0.8095 (tpt) REVERT: B 416 MET cc_start: 0.9210 (mmm) cc_final: 0.8986 (mmp) REVERT: B 434 MET cc_start: 0.9459 (mpp) cc_final: 0.9118 (mpp) REVERT: A 83 PHE cc_start: 0.9373 (m-80) cc_final: 0.8852 (t80) REVERT: A 137 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.9300 (tt0) REVERT: A 252 MET cc_start: 0.9405 (tpt) cc_final: 0.8920 (tpt) REVERT: A 376 MET cc_start: 0.8880 (tmm) cc_final: 0.8644 (tmm) REVERT: A 408 ASN cc_start: 0.8460 (m-40) cc_final: 0.7553 (t0) REVERT: A 416 MET cc_start: 0.9412 (ppp) cc_final: 0.9156 (tmm) REVERT: C 220 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9457 (mm) REVERT: C 288 TYR cc_start: 0.9148 (t80) cc_final: 0.8942 (t80) REVERT: C 304 LEU cc_start: 0.9330 (tp) cc_final: 0.9097 (pt) REVERT: C 380 HIS cc_start: 0.9372 (OUTLIER) cc_final: 0.8814 (t-90) REVERT: C 452 GLN cc_start: 0.9232 (mt0) cc_final: 0.9004 (mm-40) REVERT: C 464 LEU cc_start: 0.9486 (mt) cc_final: 0.9265 (pp) REVERT: C 490 ASP cc_start: 0.9288 (m-30) cc_final: 0.8608 (m-30) REVERT: C 646 SER cc_start: 0.9716 (m) cc_final: 0.9365 (p) REVERT: C 664 MET cc_start: 0.9665 (tmm) cc_final: 0.9395 (tmm) REVERT: C 732 LEU cc_start: 0.9763 (mt) cc_final: 0.9493 (pp) REVERT: C 786 ILE cc_start: 0.9613 (tp) cc_final: 0.9224 (pt) REVERT: D 52 ARG cc_start: 0.8392 (ttt180) cc_final: 0.7498 (ttt180) REVERT: D 121 ARG cc_start: 0.9623 (mmm160) cc_final: 0.9287 (mmm160) REVERT: D 143 ARG cc_start: 0.9596 (ttm170) cc_final: 0.9174 (ttp80) REVERT: D 159 GLU cc_start: 0.9627 (tp30) cc_final: 0.9263 (tp30) REVERT: D 300 MET cc_start: 0.9438 (mmp) cc_final: 0.8708 (mmp) REVERT: D 385 MET cc_start: 0.9338 (tpt) cc_final: 0.9067 (tpt) REVERT: D 579 MET cc_start: 0.9431 (mmm) cc_final: 0.9130 (mmm) REVERT: D 653 ASP cc_start: 0.9320 (t0) cc_final: 0.9055 (p0) outliers start: 53 outliers final: 34 residues processed: 302 average time/residue: 0.1165 time to fit residues: 56.4887 Evaluate side-chains 277 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 69 optimal weight: 0.2980 chunk 159 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 HIS A 355 ASN C 380 HIS ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN D 648 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.046837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035066 restraints weight = 118155.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.036376 restraints weight = 77987.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037360 restraints weight = 58015.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.038085 restraints weight = 46256.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.038646 restraints weight = 38829.040| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18709 Z= 0.145 Angle : 0.702 13.095 25330 Z= 0.350 Chirality : 0.044 0.274 2823 Planarity : 0.004 0.075 3258 Dihedral : 5.735 99.434 2478 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.84 % Allowed : 17.29 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2229 helix: 0.87 (0.15), residues: 1203 sheet: -0.46 (0.38), residues: 178 loop : -1.40 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 597 TYR 0.023 0.001 TYR A 185 PHE 0.019 0.001 PHE C 216 TRP 0.013 0.001 TRP B 22 HIS 0.016 0.001 HIS D 433 Details of bonding type rmsd covalent geometry : bond 0.00300 (18709) covalent geometry : angle 0.70242 (25330) hydrogen bonds : bond 0.04844 ( 981) hydrogen bonds : angle 4.95974 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 0.690 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: B 120 LEU cc_start: 0.9396 (mt) cc_final: 0.8917 (tt) REVERT: B 124 ASP cc_start: 0.9153 (m-30) cc_final: 0.8922 (m-30) REVERT: B 289 HIS cc_start: 0.9016 (m90) cc_final: 0.8387 (m90) REVERT: B 293 ASP cc_start: 0.9499 (m-30) cc_final: 0.9122 (t0) REVERT: B 297 ASP cc_start: 0.9543 (m-30) cc_final: 0.9279 (m-30) REVERT: B 380 MET cc_start: 0.8876 (ttp) cc_final: 0.8081 (tpt) REVERT: B 416 MET cc_start: 0.9190 (mmm) cc_final: 0.8972 (mmp) REVERT: B 434 MET cc_start: 0.9479 (mpp) cc_final: 0.9151 (mpp) REVERT: A 15 ASN cc_start: 0.9284 (m-40) cc_final: 0.8560 (m110) REVERT: A 83 PHE cc_start: 0.9337 (m-80) cc_final: 0.8793 (t80) REVERT: A 252 MET cc_start: 0.9406 (tpt) cc_final: 0.8908 (tpt) REVERT: A 408 ASN cc_start: 0.8405 (m-40) cc_final: 0.7574 (t0) REVERT: A 416 MET cc_start: 0.9398 (ppp) cc_final: 0.9141 (tmm) REVERT: C 220 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9439 (mm) REVERT: C 249 MET cc_start: 0.9126 (mmp) cc_final: 0.8918 (tpp) REVERT: C 298 CYS cc_start: 0.9767 (OUTLIER) cc_final: 0.9359 (p) REVERT: C 304 LEU cc_start: 0.9342 (tp) cc_final: 0.9129 (pt) REVERT: C 347 MET cc_start: 0.9117 (ppp) cc_final: 0.8873 (ppp) REVERT: C 380 HIS cc_start: 0.9405 (OUTLIER) cc_final: 0.9118 (t70) REVERT: C 490 ASP cc_start: 0.9241 (m-30) cc_final: 0.8945 (m-30) REVERT: C 603 GLU cc_start: 0.8643 (tp30) cc_final: 0.8324 (tp30) REVERT: C 646 SER cc_start: 0.9595 (m) cc_final: 0.9168 (p) REVERT: C 664 MET cc_start: 0.9695 (tmm) cc_final: 0.9394 (tmm) REVERT: C 732 LEU cc_start: 0.9766 (mt) cc_final: 0.9459 (pp) REVERT: C 786 ILE cc_start: 0.9613 (tp) cc_final: 0.9228 (pt) REVERT: D 121 ARG cc_start: 0.9630 (mmm160) cc_final: 0.9247 (mmm160) REVERT: D 123 TYR cc_start: 0.8902 (t80) cc_final: 0.8640 (t80) REVERT: D 133 MET cc_start: 0.9562 (ppp) cc_final: 0.9290 (ppp) REVERT: D 143 ARG cc_start: 0.9598 (ttm170) cc_final: 0.9217 (ttp80) REVERT: D 159 GLU cc_start: 0.9655 (tp30) cc_final: 0.9252 (tp30) REVERT: D 186 MET cc_start: 0.9639 (ptp) cc_final: 0.9419 (ptp) REVERT: D 231 MET cc_start: 0.5792 (ptp) cc_final: 0.5579 (ptp) REVERT: D 300 MET cc_start: 0.9425 (mmp) cc_final: 0.8735 (mmp) REVERT: D 385 MET cc_start: 0.9306 (tpt) cc_final: 0.8977 (tpt) REVERT: D 426 PHE cc_start: 0.9130 (m-80) cc_final: 0.8393 (m-80) REVERT: D 483 MET cc_start: 0.8614 (ptp) cc_final: 0.7953 (ptp) REVERT: D 579 MET cc_start: 0.9467 (mmm) cc_final: 0.9200 (mmm) REVERT: D 586 LEU cc_start: 0.9864 (tp) cc_final: 0.9602 (mt) REVERT: D 604 MET cc_start: 0.9483 (ppp) cc_final: 0.8996 (ppp) REVERT: D 605 ASP cc_start: 0.9573 (t0) cc_final: 0.9291 (m-30) REVERT: D 653 ASP cc_start: 0.9281 (t0) cc_final: 0.9026 (p0) REVERT: D 684 MET cc_start: 0.9417 (mmm) cc_final: 0.9152 (mmm) REVERT: D 700 PHE cc_start: 0.9575 (m-10) cc_final: 0.9367 (m-80) outliers start: 38 outliers final: 29 residues processed: 295 average time/residue: 0.1116 time to fit residues: 53.7241 Evaluate side-chains 286 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 614 PHE Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 52 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 210 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 HIS C 380 HIS ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.034432 restraints weight = 118250.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035732 restraints weight = 77881.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.036682 restraints weight = 57948.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037410 restraints weight = 46359.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.037960 restraints weight = 38864.593| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18709 Z= 0.172 Angle : 0.705 12.851 25330 Z= 0.352 Chirality : 0.044 0.277 2823 Planarity : 0.004 0.071 3258 Dihedral : 5.605 96.826 2478 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.42 % Allowed : 18.64 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2229 helix: 0.88 (0.15), residues: 1218 sheet: -0.50 (0.39), residues: 163 loop : -1.44 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 262 TYR 0.016 0.001 TYR C 651 PHE 0.018 0.001 PHE C 216 TRP 0.012 0.001 TRP A 105 HIS 0.013 0.001 HIS D 433 Details of bonding type rmsd covalent geometry : bond 0.00347 (18709) covalent geometry : angle 0.70484 (25330) hydrogen bonds : bond 0.04696 ( 981) hydrogen bonds : angle 4.95410 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 0.763 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: B 120 LEU cc_start: 0.9400 (mt) cc_final: 0.8920 (tt) REVERT: B 124 ASP cc_start: 0.9165 (m-30) cc_final: 0.8925 (m-30) REVERT: B 137 GLN cc_start: 0.9455 (mt0) cc_final: 0.9074 (mm-40) REVERT: B 289 HIS cc_start: 0.8996 (m90) cc_final: 0.8385 (m90) REVERT: B 293 ASP cc_start: 0.9624 (m-30) cc_final: 0.8995 (t0) REVERT: B 297 ASP cc_start: 0.9645 (m-30) cc_final: 0.9260 (m-30) REVERT: B 380 MET cc_start: 0.8930 (ttp) cc_final: 0.8194 (tpp) REVERT: B 416 MET cc_start: 0.9190 (mmm) cc_final: 0.8975 (mmp) REVERT: B 434 MET cc_start: 0.9490 (mpp) cc_final: 0.9167 (mpp) REVERT: A 15 ASN cc_start: 0.9331 (m-40) cc_final: 0.8629 (m110) REVERT: A 83 PHE cc_start: 0.9360 (m-80) cc_final: 0.8824 (t80) REVERT: A 243 ARG cc_start: 0.9494 (mtm-85) cc_final: 0.9054 (mtm110) REVERT: A 252 MET cc_start: 0.9409 (tpt) cc_final: 0.8931 (tpt) REVERT: A 408 ASN cc_start: 0.8431 (m-40) cc_final: 0.7599 (t0) REVERT: A 416 MET cc_start: 0.9415 (ppp) cc_final: 0.9164 (tmm) REVERT: C 220 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9432 (mm) REVERT: C 298 CYS cc_start: 0.9766 (OUTLIER) cc_final: 0.9370 (p) REVERT: C 304 LEU cc_start: 0.9356 (tp) cc_final: 0.9149 (pt) REVERT: C 347 MET cc_start: 0.9117 (ppp) cc_final: 0.8867 (ppp) REVERT: C 603 GLU cc_start: 0.8723 (tp30) cc_final: 0.8363 (tp30) REVERT: C 646 SER cc_start: 0.9462 (m) cc_final: 0.9236 (p) REVERT: C 664 MET cc_start: 0.9699 (tmm) cc_final: 0.9430 (tmm) REVERT: C 732 LEU cc_start: 0.9769 (mt) cc_final: 0.9567 (tt) REVERT: C 786 ILE cc_start: 0.9605 (tp) cc_final: 0.9232 (pt) REVERT: D 121 ARG cc_start: 0.9612 (mmm160) cc_final: 0.9181 (mmm160) REVERT: D 159 GLU cc_start: 0.9651 (tp30) cc_final: 0.9243 (tp30) REVERT: D 266 MET cc_start: 0.9751 (tmm) cc_final: 0.9528 (tmm) REVERT: D 269 LYS cc_start: 0.9384 (tptt) cc_final: 0.9004 (pttt) REVERT: D 300 MET cc_start: 0.9402 (mmp) cc_final: 0.8717 (mmp) REVERT: D 385 MET cc_start: 0.9381 (tpt) cc_final: 0.9064 (tpt) REVERT: D 420 LYS cc_start: 0.9721 (pttt) cc_final: 0.9519 (pttm) REVERT: D 449 HIS cc_start: 0.7434 (m-70) cc_final: 0.7200 (m-70) REVERT: D 483 MET cc_start: 0.8626 (ptp) cc_final: 0.7894 (ptp) REVERT: D 579 MET cc_start: 0.9473 (mmm) cc_final: 0.9138 (mmm) REVERT: D 586 LEU cc_start: 0.9864 (tp) cc_final: 0.9560 (mt) REVERT: D 589 GLN cc_start: 0.9488 (OUTLIER) cc_final: 0.9218 (mm-40) REVERT: D 601 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9293 (tm-30) REVERT: D 653 ASP cc_start: 0.9252 (t0) cc_final: 0.9024 (p0) REVERT: D 684 MET cc_start: 0.9425 (mmm) cc_final: 0.9162 (mmm) REVERT: D 700 PHE cc_start: 0.9567 (m-10) cc_final: 0.9358 (m-80) REVERT: D 717 LEU cc_start: 0.9304 (mm) cc_final: 0.9060 (mp) outliers start: 50 outliers final: 37 residues processed: 295 average time/residue: 0.1227 time to fit residues: 57.7709 Evaluate side-chains 295 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 614 PHE Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 589 GLN Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 181 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 27 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 92 optimal weight: 0.0570 chunk 57 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN A 29 HIS ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.035775 restraints weight = 114585.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.037109 restraints weight = 76112.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038105 restraints weight = 56676.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.038845 restraints weight = 45181.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039420 restraints weight = 37860.422| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18709 Z= 0.121 Angle : 0.724 14.704 25330 Z= 0.345 Chirality : 0.044 0.279 2823 Planarity : 0.004 0.072 3258 Dihedral : 5.361 93.948 2478 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.99 % Allowed : 19.61 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2229 helix: 1.10 (0.15), residues: 1214 sheet: -0.43 (0.38), residues: 176 loop : -1.28 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 59 TYR 0.024 0.001 TYR D 588 PHE 0.023 0.001 PHE C 805 TRP 0.012 0.001 TRP A 105 HIS 0.010 0.001 HIS D 433 Details of bonding type rmsd covalent geometry : bond 0.00250 (18709) covalent geometry : angle 0.72422 (25330) hydrogen bonds : bond 0.04456 ( 981) hydrogen bonds : angle 4.72652 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 0.653 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: B 120 LEU cc_start: 0.9344 (mt) cc_final: 0.8857 (tt) REVERT: B 124 ASP cc_start: 0.9123 (m-30) cc_final: 0.8900 (m-30) REVERT: B 137 GLN cc_start: 0.9463 (mt0) cc_final: 0.9148 (mp10) REVERT: B 289 HIS cc_start: 0.9043 (m90) cc_final: 0.8444 (m90) REVERT: B 293 ASP cc_start: 0.9573 (m-30) cc_final: 0.9040 (t0) REVERT: B 297 ASP cc_start: 0.9623 (m-30) cc_final: 0.9267 (m-30) REVERT: B 380 MET cc_start: 0.8929 (ttp) cc_final: 0.8266 (tpp) REVERT: B 416 MET cc_start: 0.9182 (mmm) cc_final: 0.8958 (mmp) REVERT: A 83 PHE cc_start: 0.9301 (m-80) cc_final: 0.8751 (t80) REVERT: A 243 ARG cc_start: 0.9580 (mtm-85) cc_final: 0.9054 (mtm110) REVERT: A 252 MET cc_start: 0.9400 (tpt) cc_final: 0.8973 (tpt) REVERT: A 352 MET cc_start: 0.8880 (pmm) cc_final: 0.8606 (pmm) REVERT: A 408 ASN cc_start: 0.8337 (m-40) cc_final: 0.7535 (t0) REVERT: C 220 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9410 (mm) REVERT: C 225 PHE cc_start: 0.9606 (m-10) cc_final: 0.9366 (m-10) REVERT: C 304 LEU cc_start: 0.9354 (tp) cc_final: 0.9151 (pt) REVERT: C 347 MET cc_start: 0.9094 (ppp) cc_final: 0.8802 (ppp) REVERT: C 452 GLN cc_start: 0.9267 (mt0) cc_final: 0.9019 (mm-40) REVERT: C 591 TRP cc_start: 0.9207 (t-100) cc_final: 0.8748 (t-100) REVERT: C 603 GLU cc_start: 0.8659 (tp30) cc_final: 0.8243 (tp30) REVERT: C 605 LEU cc_start: 0.9790 (OUTLIER) cc_final: 0.9508 (mp) REVERT: C 646 SER cc_start: 0.9438 (m) cc_final: 0.9206 (p) REVERT: C 664 MET cc_start: 0.9715 (tmm) cc_final: 0.9404 (tmm) REVERT: C 732 LEU cc_start: 0.9765 (mt) cc_final: 0.9409 (pp) REVERT: D 121 ARG cc_start: 0.9620 (mmm160) cc_final: 0.9175 (mmm160) REVERT: D 133 MET cc_start: 0.9460 (ppp) cc_final: 0.9189 (ppp) REVERT: D 143 ARG cc_start: 0.9657 (ttm170) cc_final: 0.9261 (ttp80) REVERT: D 159 GLU cc_start: 0.9664 (tp30) cc_final: 0.9226 (tp30) REVERT: D 167 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7381 (m110) REVERT: D 300 MET cc_start: 0.9374 (mmp) cc_final: 0.8574 (mmp) REVERT: D 385 MET cc_start: 0.9368 (tpt) cc_final: 0.9063 (tpt) REVERT: D 449 HIS cc_start: 0.7332 (m-70) cc_final: 0.7111 (m-70) REVERT: D 483 MET cc_start: 0.8633 (ptp) cc_final: 0.7823 (ptp) REVERT: D 579 MET cc_start: 0.9496 (mmm) cc_final: 0.9212 (mmm) REVERT: D 601 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9278 (tm-30) REVERT: D 653 ASP cc_start: 0.9251 (t0) cc_final: 0.9036 (p0) REVERT: D 684 MET cc_start: 0.9408 (mmm) cc_final: 0.9151 (mmm) REVERT: D 713 MET cc_start: 0.9177 (mmm) cc_final: 0.8899 (mmm) REVERT: D 717 LEU cc_start: 0.9266 (mm) cc_final: 0.8981 (pt) outliers start: 41 outliers final: 29 residues processed: 307 average time/residue: 0.1258 time to fit residues: 61.1126 Evaluate side-chains 288 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 614 PHE Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 167 ASN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN A 29 HIS ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN ** D 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.034490 restraints weight = 118705.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035777 restraints weight = 78329.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036757 restraints weight = 58109.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037480 restraints weight = 46074.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.038017 restraints weight = 38561.373| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18709 Z= 0.181 Angle : 0.738 12.265 25330 Z= 0.365 Chirality : 0.045 0.271 2823 Planarity : 0.004 0.068 3258 Dihedral : 5.443 93.140 2478 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.62 % Allowed : 19.90 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2229 helix: 1.04 (0.15), residues: 1225 sheet: -0.53 (0.39), residues: 175 loop : -1.37 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 262 TYR 0.017 0.002 TYR B 292 PHE 0.056 0.002 PHE D 700 TRP 0.012 0.001 TRP A 105 HIS 0.016 0.001 HIS D 433 Details of bonding type rmsd covalent geometry : bond 0.00366 (18709) covalent geometry : angle 0.73751 (25330) hydrogen bonds : bond 0.04563 ( 981) hydrogen bonds : angle 4.87269 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 0.561 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: B 28 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7924 (mp0) REVERT: B 120 LEU cc_start: 0.9349 (mt) cc_final: 0.8857 (tt) REVERT: B 124 ASP cc_start: 0.9163 (m-30) cc_final: 0.8922 (m-30) REVERT: B 289 HIS cc_start: 0.9050 (m90) cc_final: 0.8472 (m90) REVERT: B 293 ASP cc_start: 0.9633 (m-30) cc_final: 0.9046 (t0) REVERT: B 297 ASP cc_start: 0.9651 (m-30) cc_final: 0.9287 (m-30) REVERT: B 416 MET cc_start: 0.9216 (mmm) cc_final: 0.9010 (mmp) REVERT: A 15 ASN cc_start: 0.9351 (m-40) cc_final: 0.8677 (m110) REVERT: A 83 PHE cc_start: 0.9367 (m-80) cc_final: 0.8869 (t80) REVERT: A 137 GLN cc_start: 0.9574 (tt0) cc_final: 0.9151 (mm-40) REVERT: A 243 ARG cc_start: 0.9546 (mtm-85) cc_final: 0.9032 (mtm110) REVERT: A 252 MET cc_start: 0.9427 (tpt) cc_final: 0.8966 (tpt) REVERT: A 352 MET cc_start: 0.8903 (pmm) cc_final: 0.8609 (pmm) REVERT: A 388 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8905 (tm-30) REVERT: A 408 ASN cc_start: 0.8449 (m-40) cc_final: 0.7601 (t0) REVERT: C 225 PHE cc_start: 0.9624 (m-10) cc_final: 0.9407 (m-10) REVERT: C 249 MET cc_start: 0.9165 (tpp) cc_final: 0.8910 (tpt) REVERT: C 298 CYS cc_start: 0.9772 (OUTLIER) cc_final: 0.9366 (p) REVERT: C 304 LEU cc_start: 0.9381 (tp) cc_final: 0.9168 (pt) REVERT: C 347 MET cc_start: 0.9118 (ppp) cc_final: 0.8848 (ppp) REVERT: C 404 MET cc_start: 0.9308 (mpp) cc_final: 0.9093 (mpp) REVERT: C 452 GLN cc_start: 0.9310 (mt0) cc_final: 0.9018 (mm-40) REVERT: C 591 TRP cc_start: 0.9278 (t-100) cc_final: 0.8914 (t-100) REVERT: C 603 GLU cc_start: 0.8750 (tp30) cc_final: 0.8347 (tp30) REVERT: C 605 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9516 (mp) REVERT: C 646 SER cc_start: 0.9447 (m) cc_final: 0.9223 (p) REVERT: C 664 MET cc_start: 0.9705 (tmm) cc_final: 0.9437 (tmm) REVERT: C 732 LEU cc_start: 0.9761 (mt) cc_final: 0.9534 (tt) REVERT: D 121 ARG cc_start: 0.9609 (mmm160) cc_final: 0.9263 (mmm160) REVERT: D 159 GLU cc_start: 0.9659 (tp30) cc_final: 0.9234 (tp30) REVERT: D 167 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7627 (m-40) REVERT: D 300 MET cc_start: 0.9370 (mmp) cc_final: 0.8583 (mmp) REVERT: D 385 MET cc_start: 0.9421 (tpt) cc_final: 0.9149 (tpt) REVERT: D 426 PHE cc_start: 0.9037 (m-80) cc_final: 0.8509 (m-80) REVERT: D 449 HIS cc_start: 0.7443 (m-70) cc_final: 0.7203 (m-70) REVERT: D 579 MET cc_start: 0.9488 (mmm) cc_final: 0.9168 (mmm) REVERT: D 586 LEU cc_start: 0.9774 (tp) cc_final: 0.9410 (mt) REVERT: D 684 MET cc_start: 0.9451 (mmm) cc_final: 0.9204 (mmm) REVERT: D 713 MET cc_start: 0.9274 (mmm) cc_final: 0.9011 (mmm) REVERT: D 717 LEU cc_start: 0.9255 (mm) cc_final: 0.8996 (pt) outliers start: 54 outliers final: 40 residues processed: 290 average time/residue: 0.1172 time to fit residues: 54.4962 Evaluate side-chains 286 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 614 PHE Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 167 ASN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 104 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 0.0000 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 HIS A 186 ASN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.047185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.035553 restraints weight = 117239.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036899 restraints weight = 77414.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.037899 restraints weight = 57173.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038628 restraints weight = 45406.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039174 restraints weight = 38003.521| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18709 Z= 0.124 Angle : 0.760 15.400 25330 Z= 0.360 Chirality : 0.045 0.340 2823 Planarity : 0.004 0.071 3258 Dihedral : 5.310 91.910 2478 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.94 % Allowed : 21.02 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2229 helix: 1.20 (0.15), residues: 1209 sheet: -0.44 (0.38), residues: 176 loop : -1.23 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 329 TYR 0.018 0.001 TYR C 400 PHE 0.049 0.001 PHE D 700 TRP 0.011 0.001 TRP A 105 HIS 0.012 0.001 HIS D 433 Details of bonding type rmsd covalent geometry : bond 0.00261 (18709) covalent geometry : angle 0.75953 (25330) hydrogen bonds : bond 0.04381 ( 981) hydrogen bonds : angle 4.71595 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.702 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: B 120 LEU cc_start: 0.9330 (mt) cc_final: 0.8834 (tt) REVERT: B 124 ASP cc_start: 0.9138 (m-30) cc_final: 0.8913 (m-30) REVERT: B 289 HIS cc_start: 0.9104 (m90) cc_final: 0.8469 (m90) REVERT: B 293 ASP cc_start: 0.9606 (m-30) cc_final: 0.9010 (t0) REVERT: B 297 ASP cc_start: 0.9622 (m-30) cc_final: 0.9246 (m-30) REVERT: B 416 MET cc_start: 0.9176 (mmm) cc_final: 0.8963 (mmp) REVERT: A 15 ASN cc_start: 0.9283 (m-40) cc_final: 0.8614 (m110) REVERT: A 69 MET cc_start: 0.9407 (mmm) cc_final: 0.8354 (mmm) REVERT: A 83 PHE cc_start: 0.9327 (m-80) cc_final: 0.8805 (t80) REVERT: A 137 GLN cc_start: 0.9588 (tt0) cc_final: 0.9176 (mm-40) REVERT: A 243 ARG cc_start: 0.9528 (mtm-85) cc_final: 0.8979 (mtm110) REVERT: A 252 MET cc_start: 0.9426 (tpt) cc_final: 0.9000 (tpt) REVERT: A 310 MET cc_start: 0.5327 (mmt) cc_final: 0.4913 (mmt) REVERT: A 335 MET cc_start: 0.9515 (mpp) cc_final: 0.8805 (tpt) REVERT: A 352 MET cc_start: 0.8893 (pmm) cc_final: 0.7804 (pmm) REVERT: A 408 ASN cc_start: 0.8395 (m-40) cc_final: 0.7588 (t0) REVERT: C 225 PHE cc_start: 0.9542 (m-10) cc_final: 0.9313 (m-10) REVERT: C 229 LEU cc_start: 0.9521 (mm) cc_final: 0.9264 (mt) REVERT: C 249 MET cc_start: 0.9161 (tpp) cc_final: 0.8947 (tpt) REVERT: C 304 LEU cc_start: 0.9374 (tp) cc_final: 0.9156 (pt) REVERT: C 347 MET cc_start: 0.9092 (ppp) cc_final: 0.8813 (ppp) REVERT: C 404 MET cc_start: 0.9325 (mpp) cc_final: 0.9089 (mpp) REVERT: C 452 GLN cc_start: 0.9267 (mt0) cc_final: 0.8994 (mm-40) REVERT: C 591 TRP cc_start: 0.9251 (t-100) cc_final: 0.8909 (t-100) REVERT: C 605 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9549 (mp) REVERT: C 646 SER cc_start: 0.9423 (m) cc_final: 0.9207 (p) REVERT: C 664 MET cc_start: 0.9716 (tmm) cc_final: 0.9476 (tmm) REVERT: C 732 LEU cc_start: 0.9760 (mt) cc_final: 0.9415 (pp) REVERT: D 121 ARG cc_start: 0.9636 (mmm160) cc_final: 0.9250 (mmm160) REVERT: D 159 GLU cc_start: 0.9670 (tp30) cc_final: 0.9233 (tp30) REVERT: D 300 MET cc_start: 0.9350 (mmp) cc_final: 0.8575 (mmp) REVERT: D 385 MET cc_start: 0.9415 (tpt) cc_final: 0.9125 (tpt) REVERT: D 426 PHE cc_start: 0.8999 (m-80) cc_final: 0.8439 (m-80) REVERT: D 441 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9341 (mmmm) REVERT: D 449 HIS cc_start: 0.7400 (m-70) cc_final: 0.7114 (m-70) REVERT: D 579 MET cc_start: 0.9544 (mmm) cc_final: 0.9277 (mmm) REVERT: D 586 LEU cc_start: 0.9749 (tp) cc_final: 0.9350 (mt) REVERT: D 648 ASN cc_start: 0.9729 (OUTLIER) cc_final: 0.9469 (t0) REVERT: D 684 MET cc_start: 0.9463 (mmm) cc_final: 0.9197 (mmm) REVERT: D 713 MET cc_start: 0.9273 (mmm) cc_final: 0.8983 (mmm) REVERT: D 717 LEU cc_start: 0.9250 (mm) cc_final: 0.8981 (pt) outliers start: 40 outliers final: 30 residues processed: 289 average time/residue: 0.1179 time to fit residues: 55.1912 Evaluate side-chains 282 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 614 PHE Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 648 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 145 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN A 29 HIS ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.047092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035384 restraints weight = 116992.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036749 restraints weight = 76785.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.037746 restraints weight = 56531.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038479 restraints weight = 44982.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039056 restraints weight = 37688.270| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18709 Z= 0.128 Angle : 0.767 14.832 25330 Z= 0.365 Chirality : 0.046 0.374 2823 Planarity : 0.004 0.071 3258 Dihedral : 5.238 90.362 2478 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.03 % Allowed : 21.16 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 2229 helix: 1.19 (0.15), residues: 1216 sheet: -0.37 (0.39), residues: 177 loop : -1.16 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 333 TYR 0.017 0.001 TYR C 400 PHE 0.045 0.001 PHE D 700 TRP 0.011 0.001 TRP A 105 HIS 0.015 0.001 HIS D 433 Details of bonding type rmsd covalent geometry : bond 0.00272 (18709) covalent geometry : angle 0.76739 (25330) hydrogen bonds : bond 0.04330 ( 981) hydrogen bonds : angle 4.73038 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.624 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: B 120 LEU cc_start: 0.9323 (mt) cc_final: 0.8822 (tt) REVERT: B 124 ASP cc_start: 0.9139 (m-30) cc_final: 0.8913 (m-30) REVERT: B 289 HIS cc_start: 0.9137 (m90) cc_final: 0.8501 (m90) REVERT: B 293 ASP cc_start: 0.9603 (m-30) cc_final: 0.9066 (t0) REVERT: B 297 ASP cc_start: 0.9607 (m-30) cc_final: 0.9201 (m-30) REVERT: B 416 MET cc_start: 0.9192 (mmm) cc_final: 0.8989 (mmp) REVERT: A 15 ASN cc_start: 0.9295 (m-40) cc_final: 0.8633 (m110) REVERT: A 83 PHE cc_start: 0.9337 (m-80) cc_final: 0.8833 (t80) REVERT: A 243 ARG cc_start: 0.9498 (mtm-85) cc_final: 0.8954 (mtm110) REVERT: A 252 MET cc_start: 0.9411 (tpt) cc_final: 0.9007 (tpt) REVERT: A 310 MET cc_start: 0.5423 (mmt) cc_final: 0.5085 (mmt) REVERT: A 335 MET cc_start: 0.9517 (mpp) cc_final: 0.8894 (tpt) REVERT: A 352 MET cc_start: 0.8920 (pmm) cc_final: 0.7894 (pmm) REVERT: A 408 ASN cc_start: 0.8382 (m-40) cc_final: 0.7553 (t0) REVERT: C 229 LEU cc_start: 0.9521 (mm) cc_final: 0.9260 (mt) REVERT: C 249 MET cc_start: 0.9208 (tpp) cc_final: 0.8991 (tpt) REVERT: C 304 LEU cc_start: 0.9396 (tp) cc_final: 0.9172 (pt) REVERT: C 347 MET cc_start: 0.9080 (ppp) cc_final: 0.8801 (ppp) REVERT: C 404 MET cc_start: 0.9329 (mpp) cc_final: 0.9084 (mpp) REVERT: C 452 GLN cc_start: 0.9283 (mt0) cc_final: 0.9011 (mm-40) REVERT: C 591 TRP cc_start: 0.9270 (t-100) cc_final: 0.8853 (t-100) REVERT: C 605 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9537 (mp) REVERT: C 646 SER cc_start: 0.9428 (m) cc_final: 0.9214 (p) REVERT: C 664 MET cc_start: 0.9724 (tmm) cc_final: 0.9471 (tmm) REVERT: C 723 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9152 (mm-30) REVERT: C 732 LEU cc_start: 0.9757 (mt) cc_final: 0.9421 (pp) REVERT: C 735 ILE cc_start: 0.9369 (mm) cc_final: 0.9161 (mm) REVERT: D 121 ARG cc_start: 0.9631 (mmm160) cc_final: 0.9270 (mmm160) REVERT: D 124 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.8731 (mt-10) REVERT: D 159 GLU cc_start: 0.9663 (tp30) cc_final: 0.9221 (tp30) REVERT: D 300 MET cc_start: 0.9351 (mmp) cc_final: 0.8575 (mmp) REVERT: D 385 MET cc_start: 0.9442 (tpt) cc_final: 0.9204 (tpt) REVERT: D 426 PHE cc_start: 0.9030 (m-80) cc_final: 0.8464 (m-80) REVERT: D 441 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9324 (mmmm) REVERT: D 449 HIS cc_start: 0.7405 (m-70) cc_final: 0.7107 (m-70) REVERT: D 483 MET cc_start: 0.8657 (ptp) cc_final: 0.8376 (pmm) REVERT: D 579 MET cc_start: 0.9558 (mmm) cc_final: 0.9288 (mmm) REVERT: D 586 LEU cc_start: 0.9742 (tp) cc_final: 0.9341 (mt) REVERT: D 648 ASN cc_start: 0.9716 (OUTLIER) cc_final: 0.9476 (t0) REVERT: D 684 MET cc_start: 0.9463 (mmm) cc_final: 0.9188 (mmm) REVERT: D 713 MET cc_start: 0.9281 (mmm) cc_final: 0.8986 (mmm) REVERT: D 717 LEU cc_start: 0.9262 (mm) cc_final: 0.8973 (pt) REVERT: D 809 TYR cc_start: 0.7985 (m-10) cc_final: 0.7654 (m-80) outliers start: 42 outliers final: 35 residues processed: 295 average time/residue: 0.1195 time to fit residues: 56.1347 Evaluate side-chains 294 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 614 PHE Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 648 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 138 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 156 optimal weight: 0.0020 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 ASN D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.047312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035605 restraints weight = 116944.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.036962 restraints weight = 76910.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037960 restraints weight = 56829.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038705 restraints weight = 45190.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039263 restraints weight = 37801.985| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18709 Z= 0.127 Angle : 0.789 14.727 25330 Z= 0.373 Chirality : 0.046 0.384 2823 Planarity : 0.004 0.069 3258 Dihedral : 5.190 89.253 2478 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.89 % Allowed : 21.40 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2229 helix: 1.21 (0.15), residues: 1212 sheet: -0.24 (0.39), residues: 177 loop : -1.14 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 329 TYR 0.029 0.001 TYR C 288 PHE 0.043 0.001 PHE D 700 TRP 0.011 0.001 TRP A 105 HIS 0.005 0.001 HIS D 433 Details of bonding type rmsd covalent geometry : bond 0.00271 (18709) covalent geometry : angle 0.78853 (25330) hydrogen bonds : bond 0.04295 ( 981) hydrogen bonds : angle 4.72433 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.752 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: B 120 LEU cc_start: 0.9306 (mt) cc_final: 0.8806 (tt) REVERT: B 124 ASP cc_start: 0.9135 (m-30) cc_final: 0.8912 (m-30) REVERT: B 289 HIS cc_start: 0.9115 (m90) cc_final: 0.8457 (m90) REVERT: B 293 ASP cc_start: 0.9615 (m-30) cc_final: 0.8992 (t0) REVERT: B 297 ASP cc_start: 0.9590 (m-30) cc_final: 0.9174 (m-30) REVERT: B 369 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9151 (mp0) REVERT: B 416 MET cc_start: 0.9180 (mmm) cc_final: 0.8975 (mmp) REVERT: A 69 MET cc_start: 0.9362 (mmm) cc_final: 0.8288 (mmm) REVERT: A 83 PHE cc_start: 0.9339 (m-80) cc_final: 0.8839 (t80) REVERT: A 137 GLN cc_start: 0.9563 (tt0) cc_final: 0.9196 (mm-40) REVERT: A 243 ARG cc_start: 0.9501 (mtm-85) cc_final: 0.9134 (mtm110) REVERT: A 252 MET cc_start: 0.9388 (tpt) cc_final: 0.8985 (tpt) REVERT: A 256 TYR cc_start: 0.9453 (m-80) cc_final: 0.9085 (m-80) REVERT: A 310 MET cc_start: 0.5471 (mmt) cc_final: 0.5194 (mmt) REVERT: A 335 MET cc_start: 0.9522 (mpp) cc_final: 0.8904 (tpt) REVERT: A 352 MET cc_start: 0.8924 (pmm) cc_final: 0.7917 (pmm) REVERT: A 408 ASN cc_start: 0.8371 (m-40) cc_final: 0.7550 (t0) REVERT: A 416 MET cc_start: 0.9472 (tmm) cc_final: 0.9264 (tmm) REVERT: C 229 LEU cc_start: 0.9516 (mm) cc_final: 0.9129 (mt) REVERT: C 269 ASN cc_start: 0.9488 (m-40) cc_final: 0.9125 (m110) REVERT: C 304 LEU cc_start: 0.9389 (tp) cc_final: 0.9165 (pt) REVERT: C 347 MET cc_start: 0.9067 (ppp) cc_final: 0.8787 (ppp) REVERT: C 404 MET cc_start: 0.9310 (mpp) cc_final: 0.9059 (mpp) REVERT: C 452 GLN cc_start: 0.9267 (mt0) cc_final: 0.8991 (mm-40) REVERT: C 591 TRP cc_start: 0.9274 (t-100) cc_final: 0.8949 (t-100) REVERT: C 605 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9532 (mp) REVERT: C 646 SER cc_start: 0.9428 (m) cc_final: 0.9122 (p) REVERT: C 650 SER cc_start: 0.9528 (t) cc_final: 0.9212 (p) REVERT: C 664 MET cc_start: 0.9771 (tmm) cc_final: 0.9472 (tmm) REVERT: C 723 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9150 (mm-30) REVERT: C 732 LEU cc_start: 0.9755 (mt) cc_final: 0.9406 (pp) REVERT: C 735 ILE cc_start: 0.9359 (mm) cc_final: 0.9148 (mm) REVERT: D 121 ARG cc_start: 0.9615 (mmm160) cc_final: 0.9287 (mmm160) REVERT: D 143 ARG cc_start: 0.9674 (ttm170) cc_final: 0.9242 (ttp80) REVERT: D 159 GLU cc_start: 0.9651 (tp30) cc_final: 0.9203 (tp30) REVERT: D 300 MET cc_start: 0.9330 (mmp) cc_final: 0.8568 (mmp) REVERT: D 441 LYS cc_start: 0.9563 (mmmm) cc_final: 0.9360 (mmmm) REVERT: D 449 HIS cc_start: 0.7437 (m-70) cc_final: 0.7134 (m-70) REVERT: D 483 MET cc_start: 0.8630 (ptp) cc_final: 0.8350 (pmm) REVERT: D 579 MET cc_start: 0.9548 (mmm) cc_final: 0.9273 (mmm) REVERT: D 586 LEU cc_start: 0.9737 (tp) cc_final: 0.9364 (mt) REVERT: D 648 ASN cc_start: 0.9700 (OUTLIER) cc_final: 0.9446 (t0) REVERT: D 684 MET cc_start: 0.9441 (mmm) cc_final: 0.9183 (mmm) REVERT: D 713 MET cc_start: 0.9280 (mmm) cc_final: 0.8975 (mmm) REVERT: D 717 LEU cc_start: 0.9267 (mm) cc_final: 0.8970 (pt) REVERT: D 809 TYR cc_start: 0.7935 (m-10) cc_final: 0.7645 (m-80) outliers start: 39 outliers final: 36 residues processed: 291 average time/residue: 0.1213 time to fit residues: 56.1523 Evaluate side-chains 299 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 614 PHE Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 648 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 111 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN C 172 ASN C 780 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN D 433 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.045250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.034017 restraints weight = 122128.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035310 restraints weight = 79956.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.036261 restraints weight = 58838.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.036960 restraints weight = 46649.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037491 restraints weight = 39007.655| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18709 Z= 0.217 Angle : 0.816 20.358 25330 Z= 0.400 Chirality : 0.047 0.343 2823 Planarity : 0.004 0.067 3258 Dihedral : 5.403 90.169 2478 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.23 % Allowed : 21.36 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2229 helix: 0.98 (0.15), residues: 1219 sheet: -0.44 (0.38), residues: 178 loop : -1.26 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 333 TYR 0.016 0.002 TYR C 651 PHE 0.038 0.002 PHE D 700 TRP 0.011 0.002 TRP A 105 HIS 0.016 0.001 HIS D 433 Details of bonding type rmsd covalent geometry : bond 0.00434 (18709) covalent geometry : angle 0.81564 (25330) hydrogen bonds : bond 0.04533 ( 981) hydrogen bonds : angle 4.99477 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.67 seconds wall clock time: 60 minutes 23.95 seconds (3623.95 seconds total)