Starting phenix.real_space_refine on Fri Sep 11 23:51:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xle_22241/09_2026/6xle_22241.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xle_22241/09_2026/6xle_22241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xle_22241/09_2026/6xle_22241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xle_22241/09_2026/6xle_22241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xle_22241/09_2026/6xle_22241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xle_22241/09_2026/6xle_22241.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xle_22241/09_2026/6xle_22241.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xle_22241/09_2026/6xle_22241.cif" } resolution = 2.74 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= -0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 22 5.16 5 C 7824 2.51 5 N 2008 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12240 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "C" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "D" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.78, per 1000 atoms: 0.23 Number of scatterers: 12240 At special positions: 0 Unit cell: (104.841, 92.133, 132.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 22 16.00 P 6 15.00 Mg 2 11.99 O 2376 8.00 N 2008 7.00 C 7824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 555.9 milliseconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 41.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 4.321A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 50 removed outlier: 3.597A pdb=" N LEU A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.614A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.903A pdb=" N LEU A 182 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.643A pdb=" N SER A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 removed outlier: 3.858A pdb=" N ILE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.602A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.892A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.624A pdb=" N VAL A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.791A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.824A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.920A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 removed outlier: 3.501A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.613A pdb=" N GLU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.668A pdb=" N LYS A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.571A pdb=" N LYS A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.504A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.492A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 50 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.528A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.666A pdb=" N TYR B 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 3.902A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.763A pdb=" N ILE B 280 " --> pdb=" O PRO B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.574A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 405 removed outlier: 3.926A pdb=" N VAL B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.683A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.508A pdb=" N ILE B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.698A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 removed outlier: 3.559A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.560A pdb=" N VAL B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 removed outlier: 4.395A pdb=" N LEU B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.508A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.632A pdb=" N LYS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 555 removed outlier: 3.577A pdb=" N ASP B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.825A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 627 removed outlier: 3.715A pdb=" N LYS B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 651 removed outlier: 3.599A pdb=" N LYS B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 641 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.605A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.982A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 removed outlier: 3.896A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 326 through 336 removed outlier: 3.580A pdb=" N GLU C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.787A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 removed outlier: 3.994A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.530A pdb=" N VAL D 328 " --> pdb=" O GLU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.626A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.508A pdb=" N GLU A 4 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.584A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 removed outlier: 4.152A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 308 removed outlier: 7.051A pdb=" N LEU A 339 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 452 removed outlier: 4.147A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 removed outlier: 3.546A pdb=" N ILE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 6.950A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 removed outlier: 4.029A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AB2, first strand: chain 'C' and resid 213 through 218 removed outlier: 7.011A pdb=" N ILE C 216 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR C 318 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU C 218 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS C 316 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 259 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.709A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 213 through 218 removed outlier: 5.642A pdb=" N THR D 214 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 221 through 222 543 hydrogen bonds defined for protein. 1488 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: 2.31 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3962 1.34 - 1.46: 2647 1.46 - 1.58: 5807 1.58 - 1.69: 10 1.69 - 1.81: 42 Bond restraints: 12468 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.581 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 12463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 16790 3.46 - 6.92: 30 6.92 - 10.39: 6 10.39 - 13.85: 2 13.85 - 17.31: 2 Bond angle restraints: 16830 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.64 17.31 3.00e+00 1.11e-01 3.33e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.85 17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.54 10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.58 10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " pdb=" O2G ANP B 801 " ideal model delta sigma weight residual 101.05 109.72 -8.67 3.00e+00 1.11e-01 8.35e+00 ... (remaining 16825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.24: 7315 18.24 - 36.49: 188 36.49 - 54.73: 36 54.73 - 72.98: 13 72.98 - 91.22: 18 Dihedral angle restraints: 7570 sinusoidal: 3166 harmonic: 4404 Sorted by residual: dihedral pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " pdb=" CG ASP B 132 " pdb=" OD1 ASP B 132 " ideal model delta sinusoidal sigma weight residual -30.00 -88.36 58.36 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -56.07 91.22 1 3.00e+01 1.11e-03 1.09e+01 dihedral pdb=" O1B ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PB ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sinusoidal sigma weight residual 35.15 -53.01 88.16 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 7567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1645 0.055 - 0.109: 207 0.109 - 0.164: 26 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1880 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1877 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 355 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO B 355 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 570 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO B 571 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 571 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 571 " -0.015 5.00e-02 4.00e+02 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 312 2.70 - 3.31: 13564 3.31 - 3.92: 24038 3.92 - 4.53: 32922 4.53 - 5.14: 51589 Nonbonded interactions: 122425 Sorted by model distance: nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.095 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.096 2.170 nonbonded pdb=" OE2 GLU B 33 " pdb="MG MG B 802 " model vdw 2.110 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.127 2.170 nonbonded pdb=" O1A ANP B 801 " pdb="MG MG B 802 " model vdw 2.213 2.170 ... (remaining 122420 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.210 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:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 12468 Z= 0.158 Angle : 0.488 17.312 16830 Z= 0.237 Chirality : 0.039 0.273 1880 Planarity : 0.003 0.035 2146 Dihedral : 9.997 91.219 4702 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.18), residues: 1482 helix: -3.59 (0.12), residues: 528 sheet: -1.42 (0.28), residues: 326 loop : -1.46 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.006 0.001 TYR A 285 PHE 0.005 0.001 PHE D 283 TRP 0.006 0.001 TRP A 273 HIS 0.001 0.000 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (12468) covalent geometry : angle 0.48833 / 0.24 (16830) hydrogen bonds : bond 0.28588 / 18.57 ( 513) hydrogen bonds : angle 9.38853 / 6.59 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.477 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.7340 time to fit residues: 278.7320 Evaluate side-chains 162 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 151 ASN A 431 ASN A 442 ASN ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN C 207 GLN C 223 ASN C 284 HIS D 303 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112278 restraints weight = 16733.524| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.84 r_work: 0.3221 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12468 Z= 0.154 Angle : 0.548 5.991 16830 Z= 0.288 Chirality : 0.043 0.158 1880 Planarity : 0.004 0.037 2146 Dihedral : 4.885 70.154 1610 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.75 % Allowed : 15.30 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.20), residues: 1482 helix: -1.35 (0.19), residues: 564 sheet: -1.26 (0.27), residues: 322 loop : -0.85 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 624 TYR 0.015 0.002 TYR A 456 PHE 0.018 0.002 PHE D 283 TRP 0.012 0.001 TRP C 285 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (12468) covalent geometry : angle 0.54838 / 0.29 (16830) hydrogen bonds : bond 0.04368 / 2.89 ( 513) hydrogen bonds : angle 5.45128 / 3.84 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7535 (pp20) REVERT: B 11 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: B 268 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7509 (mptp) REVERT: B 535 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 544 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8310 (tm-30) REVERT: D 247 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: D 331 ASN cc_start: 0.9183 (m110) cc_final: 0.8982 (m110) outliers start: 37 outliers final: 10 residues processed: 199 average time/residue: 0.6313 time to fit residues: 135.6197 Evaluate side-chains 145 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 ASN A 380 GLN A 466 ASN B 55 GLN B 92 ASN B 373 ASN B 466 ASN C 223 ASN D 314 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108117 restraints weight = 16887.572| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.87 r_work: 0.3156 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12468 Z= 0.140 Angle : 0.522 7.621 16830 Z= 0.273 Chirality : 0.042 0.142 1880 Planarity : 0.004 0.042 2146 Dihedral : 5.314 63.621 1610 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.49 % Allowed : 16.20 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.21), residues: 1482 helix: -0.35 (0.21), residues: 574 sheet: -1.07 (0.27), residues: 318 loop : -0.72 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 575 TYR 0.010 0.001 TYR A 565 PHE 0.018 0.002 PHE A 660 TRP 0.011 0.001 TRP C 285 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12468) covalent geometry : angle 0.52189 / 0.27 (16830) hydrogen bonds : bond 0.03557 / 2.35 ( 513) hydrogen bonds : angle 4.90209 / 3.45 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.491 Fit side-chains REVERT: A 349 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7664 (pp20) REVERT: B 268 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7713 (mptp) REVERT: B 312 GLU cc_start: 0.7514 (tt0) cc_final: 0.7216 (tt0) REVERT: B 398 GLU cc_start: 0.8229 (tp30) cc_final: 0.7957 (mm-30) REVERT: B 448 ASP cc_start: 0.8442 (p0) cc_final: 0.8205 (p0) REVERT: B 538 LYS cc_start: 0.8501 (pptt) cc_final: 0.8294 (ptpp) REVERT: B 548 LYS cc_start: 0.8690 (ptpt) cc_final: 0.8448 (ptpt) REVERT: B 590 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8414 (mttt) REVERT: B 637 ASP cc_start: 0.8055 (m-30) cc_final: 0.7827 (m-30) REVERT: D 247 GLN cc_start: 0.8586 (mt0) cc_final: 0.8320 (tt0) REVERT: D 316 LYS cc_start: 0.8235 (tptt) cc_final: 0.7933 (mmmt) outliers start: 47 outliers final: 14 residues processed: 188 average time/residue: 0.6324 time to fit residues: 128.2768 Evaluate side-chains 144 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 32 optimal weight: 0.0040 chunk 120 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 ASN B 197 HIS C 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107506 restraints weight = 16486.662| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.93 r_work: 0.3146 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12468 Z= 0.134 Angle : 0.502 7.244 16830 Z= 0.260 Chirality : 0.042 0.142 1880 Planarity : 0.003 0.041 2146 Dihedral : 5.352 65.849 1610 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.90 % Allowed : 17.09 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1482 helix: 0.10 (0.22), residues: 574 sheet: -0.99 (0.28), residues: 314 loop : -0.66 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.022 0.001 TYR D 230 PHE 0.015 0.001 PHE A 660 TRP 0.011 0.001 TRP A 148 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (12468) covalent geometry : angle 0.50190 / 0.26 (16830) hydrogen bonds : bond 0.03246 / 2.15 ( 513) hydrogen bonds : angle 4.75520 / 3.34 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8303 (mttt) REVERT: A 349 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7688 (pp20) REVERT: B 268 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7796 (mptp) REVERT: B 308 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: B 398 GLU cc_start: 0.8226 (tp30) cc_final: 0.7930 (mm-30) REVERT: B 448 ASP cc_start: 0.8457 (p0) cc_final: 0.8228 (p0) REVERT: B 548 LYS cc_start: 0.8668 (ptpt) cc_final: 0.8418 (ptpt) REVERT: B 590 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8414 (mttt) REVERT: D 238 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7690 (ttp-170) REVERT: D 247 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: D 278 ASP cc_start: 0.8190 (m-30) cc_final: 0.7955 (m-30) REVERT: D 316 LYS cc_start: 0.8220 (tptt) cc_final: 0.7930 (mmmt) outliers start: 39 outliers final: 13 residues processed: 164 average time/residue: 0.5921 time to fit residues: 104.9395 Evaluate side-chains 137 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 1 optimal weight: 0.0070 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 ASN A 592 GLN C 223 ASN C 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106260 restraints weight = 16570.623| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.91 r_work: 0.3120 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12468 Z= 0.147 Angle : 0.509 7.110 16830 Z= 0.264 Chirality : 0.043 0.140 1880 Planarity : 0.003 0.043 2146 Dihedral : 5.450 66.046 1610 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.19 % Allowed : 17.53 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1482 helix: 0.49 (0.22), residues: 558 sheet: -0.94 (0.28), residues: 314 loop : -0.64 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.023 0.002 TYR C 230 PHE 0.013 0.001 PHE B 6 TRP 0.010 0.001 TRP A 148 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (12468) covalent geometry : angle 0.50934 / 0.26 (16830) hydrogen bonds : bond 0.03324 / 2.20 ( 513) hydrogen bonds : angle 4.71580 / 3.32 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: A 178 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8318 (mttt) REVERT: A 349 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7794 (pp20) REVERT: A 384 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 447 VAL cc_start: 0.7943 (m) cc_final: 0.7697 (t) REVERT: A 638 LEU cc_start: 0.8612 (mt) cc_final: 0.8409 (mm) REVERT: B 268 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7803 (mptp) REVERT: B 308 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: B 398 GLU cc_start: 0.8215 (tp30) cc_final: 0.7920 (mm-30) REVERT: B 448 ASP cc_start: 0.8436 (p0) cc_final: 0.8205 (p0) REVERT: B 548 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8373 (mtmm) REVERT: B 590 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8438 (mttt) REVERT: B 606 LYS cc_start: 0.7892 (mttp) cc_final: 0.7386 (mppt) REVERT: B 623 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7121 (pttp) REVERT: D 238 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7764 (ttp-170) REVERT: D 247 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: D 278 ASP cc_start: 0.8210 (m-30) cc_final: 0.7968 (m-30) REVERT: D 316 LYS cc_start: 0.8228 (tptt) cc_final: 0.8005 (mmmt) outliers start: 43 outliers final: 13 residues processed: 171 average time/residue: 0.6875 time to fit residues: 126.0552 Evaluate side-chains 149 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106291 restraints weight = 16550.848| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.91 r_work: 0.3128 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12468 Z= 0.138 Angle : 0.501 6.570 16830 Z= 0.260 Chirality : 0.042 0.139 1880 Planarity : 0.003 0.044 2146 Dihedral : 5.442 66.251 1610 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.12 % Allowed : 17.83 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1482 helix: 0.65 (0.23), residues: 552 sheet: -0.98 (0.28), residues: 314 loop : -0.57 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.023 0.002 TYR C 230 PHE 0.013 0.001 PHE B 6 TRP 0.012 0.001 TRP A 148 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12468) covalent geometry : angle 0.50061 / 0.26 (16830) hydrogen bonds : bond 0.03191 / 2.12 ( 513) hydrogen bonds : angle 4.64409 / 3.27 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8318 (mttt) REVERT: A 349 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7777 (pp20) REVERT: A 386 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7916 (mtmm) REVERT: A 398 GLU cc_start: 0.8275 (tp30) cc_final: 0.8014 (mm-30) REVERT: A 447 VAL cc_start: 0.7951 (m) cc_final: 0.7723 (t) REVERT: A 544 GLU cc_start: 0.8133 (tp30) cc_final: 0.7880 (tp30) REVERT: A 636 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7677 (mtpp) REVERT: A 638 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8429 (mm) REVERT: B 268 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7811 (mptp) REVERT: B 308 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6942 (mm-30) REVERT: B 398 GLU cc_start: 0.8238 (tp30) cc_final: 0.7940 (mm-30) REVERT: B 448 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8226 (p0) REVERT: B 548 LYS cc_start: 0.8623 (ptpt) cc_final: 0.8403 (mtmm) REVERT: B 590 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8445 (mttt) REVERT: B 606 LYS cc_start: 0.7930 (mttp) cc_final: 0.7414 (mppt) REVERT: B 623 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7154 (pttp) REVERT: C 247 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8317 (tp-100) REVERT: D 238 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7767 (ttp-170) REVERT: D 247 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: D 316 LYS cc_start: 0.8192 (tptt) cc_final: 0.7960 (mmmt) outliers start: 42 outliers final: 20 residues processed: 163 average time/residue: 0.6681 time to fit residues: 116.9499 Evaluate side-chains 154 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 27 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107665 restraints weight = 16459.662| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.90 r_work: 0.3149 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12468 Z= 0.110 Angle : 0.480 5.907 16830 Z= 0.250 Chirality : 0.041 0.137 1880 Planarity : 0.003 0.043 2146 Dihedral : 5.296 64.287 1610 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.53 % Allowed : 19.24 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1482 helix: 0.64 (0.22), residues: 580 sheet: -0.94 (0.27), residues: 326 loop : -0.62 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.023 0.001 TYR C 230 PHE 0.013 0.001 PHE B 6 TRP 0.013 0.001 TRP A 148 HIS 0.002 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (12468) covalent geometry : angle 0.47986 / 0.25 (16830) hydrogen bonds : bond 0.02938 / 1.95 ( 513) hydrogen bonds : angle 4.52695 / 3.19 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7779 (pp20) REVERT: A 398 GLU cc_start: 0.8237 (tp30) cc_final: 0.8002 (mm-30) REVERT: A 447 VAL cc_start: 0.7942 (m) cc_final: 0.7707 (t) REVERT: A 544 GLU cc_start: 0.8118 (tp30) cc_final: 0.7913 (tp30) REVERT: A 636 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7702 (mtpp) REVERT: A 638 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8421 (mm) REVERT: B 268 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7829 (mptp) REVERT: B 308 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6893 (mm-30) REVERT: B 398 GLU cc_start: 0.8216 (tp30) cc_final: 0.7947 (mm-30) REVERT: B 448 ASP cc_start: 0.8462 (p0) cc_final: 0.8241 (p0) REVERT: B 548 LYS cc_start: 0.8594 (ptpt) cc_final: 0.8330 (mtmm) REVERT: B 590 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8442 (mttt) REVERT: B 606 LYS cc_start: 0.7904 (mttp) cc_final: 0.7400 (mppt) REVERT: B 637 ASP cc_start: 0.8376 (m-30) cc_final: 0.8159 (m-30) REVERT: C 247 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8325 (tp-100) REVERT: C 258 LYS cc_start: 0.7904 (mtpm) cc_final: 0.7681 (mmtp) REVERT: C 316 LYS cc_start: 0.8259 (tptt) cc_final: 0.8040 (mmmt) REVERT: D 238 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7695 (ttp-170) REVERT: D 247 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: D 316 LYS cc_start: 0.8126 (tptt) cc_final: 0.7911 (mmmt) outliers start: 34 outliers final: 18 residues processed: 162 average time/residue: 0.6336 time to fit residues: 110.9168 Evaluate side-chains 148 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105656 restraints weight = 16575.237| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.91 r_work: 0.3118 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12468 Z= 0.147 Angle : 0.523 7.733 16830 Z= 0.272 Chirality : 0.043 0.135 1880 Planarity : 0.003 0.043 2146 Dihedral : 5.450 65.679 1610 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.53 % Allowed : 19.17 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1482 helix: 0.78 (0.23), residues: 558 sheet: -0.99 (0.27), residues: 328 loop : -0.59 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.024 0.002 TYR C 230 PHE 0.013 0.001 PHE B 6 TRP 0.010 0.001 TRP A 148 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (12468) covalent geometry : angle 0.52348 / 0.27 (16830) hydrogen bonds : bond 0.03208 / 2.12 ( 513) hydrogen bonds : angle 4.61587 / 3.25 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: A 178 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8314 (mttt) REVERT: A 349 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7764 (pp20) REVERT: A 386 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7874 (mtmm) REVERT: A 398 GLU cc_start: 0.8293 (tp30) cc_final: 0.8030 (mm-30) REVERT: A 447 VAL cc_start: 0.7937 (m) cc_final: 0.7720 (t) REVERT: A 544 GLU cc_start: 0.8155 (tp30) cc_final: 0.7939 (tp30) REVERT: A 636 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7743 (mtpp) REVERT: A 638 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8448 (mm) REVERT: B 268 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7800 (mptp) REVERT: B 308 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: B 398 GLU cc_start: 0.8233 (tp30) cc_final: 0.7937 (mm-30) REVERT: B 590 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8505 (mttt) REVERT: B 606 LYS cc_start: 0.7948 (mttp) cc_final: 0.7426 (mppt) REVERT: B 623 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7191 (pttp) REVERT: C 247 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8348 (tp-100) REVERT: C 258 LYS cc_start: 0.7976 (mtpm) cc_final: 0.7726 (mmtp) REVERT: C 316 LYS cc_start: 0.8318 (tptt) cc_final: 0.8077 (mmmt) REVERT: D 238 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7746 (ttp-170) REVERT: D 247 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: D 316 LYS cc_start: 0.8183 (tptt) cc_final: 0.7965 (mmmt) outliers start: 34 outliers final: 13 residues processed: 155 average time/residue: 0.6153 time to fit residues: 103.2404 Evaluate side-chains 145 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105168 restraints weight = 16554.578| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.89 r_work: 0.3108 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12468 Z= 0.161 Angle : 0.539 7.095 16830 Z= 0.279 Chirality : 0.043 0.138 1880 Planarity : 0.003 0.043 2146 Dihedral : 5.551 67.141 1610 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.45 % Allowed : 19.17 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1482 helix: 0.78 (0.23), residues: 558 sheet: -0.94 (0.27), residues: 328 loop : -0.59 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.024 0.002 TYR C 230 PHE 0.013 0.002 PHE A 410 TRP 0.010 0.001 TRP A 148 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (12468) covalent geometry : angle 0.53863 / 0.28 (16830) hydrogen bonds : bond 0.03305 / 2.19 ( 513) hydrogen bonds : angle 4.66623 / 3.28 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: A 178 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8337 (mttt) REVERT: A 349 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7800 (pp20) REVERT: A 386 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7853 (mtmm) REVERT: A 398 GLU cc_start: 0.8327 (tp30) cc_final: 0.8056 (mm-30) REVERT: A 447 VAL cc_start: 0.7985 (m) cc_final: 0.7774 (t) REVERT: A 544 GLU cc_start: 0.8109 (tp30) cc_final: 0.7872 (tp30) REVERT: A 636 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7703 (mtpp) REVERT: A 653 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8475 (p) REVERT: B 268 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7808 (mptp) REVERT: B 308 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: B 398 GLU cc_start: 0.8243 (tp30) cc_final: 0.7938 (mm-30) REVERT: B 548 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8203 (ttpp) REVERT: B 590 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8501 (mttt) REVERT: B 606 LYS cc_start: 0.7965 (mttp) cc_final: 0.7458 (mppt) REVERT: C 247 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8348 (tp-100) REVERT: C 258 LYS cc_start: 0.8034 (mtpm) cc_final: 0.7775 (mmtp) REVERT: C 316 LYS cc_start: 0.8250 (tptt) cc_final: 0.8005 (mmmt) REVERT: D 238 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7722 (ttp-170) REVERT: D 247 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8387 (tt0) outliers start: 33 outliers final: 15 residues processed: 147 average time/residue: 0.6429 time to fit residues: 101.8865 Evaluate side-chains 141 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107405 restraints weight = 16550.695| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.92 r_work: 0.3146 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12468 Z= 0.111 Angle : 0.500 7.138 16830 Z= 0.260 Chirality : 0.042 0.137 1880 Planarity : 0.003 0.043 2146 Dihedral : 5.322 64.246 1610 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.93 % Allowed : 19.69 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1482 helix: 0.76 (0.23), residues: 582 sheet: -0.88 (0.27), residues: 328 loop : -0.54 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.024 0.001 TYR C 230 PHE 0.013 0.001 PHE B 6 TRP 0.013 0.001 TRP A 148 HIS 0.002 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (12468) covalent geometry : angle 0.49962 / 0.26 (16830) hydrogen bonds : bond 0.02950 / 1.95 ( 513) hydrogen bonds : angle 4.54078 / 3.20 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8294 (mttt) REVERT: A 349 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7772 (pp20) REVERT: A 386 LYS cc_start: 0.8221 (mmmt) cc_final: 0.7845 (mtmm) REVERT: A 398 GLU cc_start: 0.8276 (tp30) cc_final: 0.8003 (mm-30) REVERT: A 447 VAL cc_start: 0.7967 (m) cc_final: 0.7767 (t) REVERT: A 544 GLU cc_start: 0.8118 (tp30) cc_final: 0.7890 (tp30) REVERT: A 636 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7686 (mtpp) REVERT: B 268 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7814 (mptp) REVERT: B 308 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: B 398 GLU cc_start: 0.8223 (tp30) cc_final: 0.7936 (mm-30) REVERT: B 502 ASP cc_start: 0.8896 (m-30) cc_final: 0.8649 (m-30) REVERT: B 548 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8174 (ttpp) REVERT: B 590 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8491 (mttt) REVERT: B 606 LYS cc_start: 0.7893 (mttp) cc_final: 0.7394 (mppt) REVERT: C 247 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8336 (tp-100) REVERT: C 258 LYS cc_start: 0.7999 (mtpm) cc_final: 0.7758 (mmtp) REVERT: C 316 LYS cc_start: 0.8259 (tptt) cc_final: 0.7982 (mmmt) REVERT: D 238 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7717 (ttp-170) REVERT: D 247 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8358 (tt0) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 0.6302 time to fit residues: 101.0068 Evaluate side-chains 142 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 77 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 137 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108314 restraints weight = 16460.497| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.91 r_work: 0.3161 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12468 Z= 0.102 Angle : 0.488 6.910 16830 Z= 0.253 Chirality : 0.041 0.135 1880 Planarity : 0.003 0.042 2146 Dihedral : 5.215 62.882 1610 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.78 % Allowed : 19.69 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1482 helix: 0.86 (0.23), residues: 582 sheet: -0.82 (0.27), residues: 328 loop : -0.50 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.024 0.001 TYR C 230 PHE 0.013 0.001 PHE B 6 TRP 0.013 0.001 TRP A 148 HIS 0.002 0.001 HIS D 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (12468) covalent geometry : angle 0.48812 / 0.25 (16830) hydrogen bonds : bond 0.02852 / 1.88 ( 513) hydrogen bonds : angle 4.44540 / 3.13 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4069.66 seconds wall clock time: 70 minutes 16.30 seconds (4216.30 seconds total)