Starting phenix.real_space_refine on Wed Jul 30 12:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xle_22241/07_2025/6xle_22241.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xle_22241/07_2025/6xle_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xle_22241/07_2025/6xle_22241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xle_22241/07_2025/6xle_22241.map" model { file = "/net/cci-nas-00/data/ceres_data/6xle_22241/07_2025/6xle_22241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xle_22241/07_2025/6xle_22241.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.67, per 1000 atoms: 0.63 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: 2.85 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.70 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: 3.95 Time building geometry restraints manager: 3.41 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: 7358 18.24 - 36.49: 195 36.49 - 54.73: 40 54.73 - 72.98: 13 72.98 - 91.22: 20 Dihedral angle restraints: 7626 sinusoidal: 3222 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 7623 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: 0.05 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: 1.020 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.410 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 10.218 91.219 4758 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP A 273 HIS 0.001 0.000 HIS D 284 PHE 0.005 0.001 PHE D 283 TYR 0.006 0.001 TYR A 285 ARG 0.001 0.000 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.28588 ( 513) hydrogen bonds : angle 9.38853 ( 1488) covalent geometry : bond 0.00312 (12468) covalent geometry : angle 0.48833 (16830) *********************** 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 : 1.316 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 1.6794 time to fit residues: 637.9027 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 : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 151 ASN A 380 GLN A 431 ASN ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN B 466 ASN B 557 GLN C 207 GLN C 223 ASN D 303 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.135474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114306 restraints weight = 16711.454| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.84 r_work: 0.3252 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12468 Z= 0.133 Angle : 0.533 6.149 16830 Z= 0.279 Chirality : 0.043 0.159 1880 Planarity : 0.004 0.038 2146 Dihedral : 5.895 73.547 1666 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.75 % Allowed : 15.23 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.20), residues: 1482 helix: -1.40 (0.19), residues: 564 sheet: -1.24 (0.27), residues: 322 loop : -0.83 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 285 HIS 0.003 0.001 HIS D 309 PHE 0.017 0.002 PHE D 283 TYR 0.014 0.002 TYR A 456 ARG 0.004 0.001 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 513) hydrogen bonds : angle 5.36083 ( 1488) covalent geometry : bond 0.00309 (12468) covalent geometry : angle 0.53289 (16830) *********************** 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 217 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7567 (pp20) REVERT: B 11 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: B 14 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7393 (tm-30) REVERT: B 268 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7503 (mptp) REVERT: B 448 ASP cc_start: 0.8316 (p0) cc_final: 0.8110 (p0) REVERT: B 535 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 544 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8261 (tm-30) REVERT: D 247 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8200 (tt0) outliers start: 37 outliers final: 12 residues processed: 204 average time/residue: 1.4041 time to fit residues: 309.5819 Evaluate side-chains 148 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 208 LEU 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 Chi-restraints excluded: chain D residue 257 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN A 431 ASN A 442 ASN A 466 ASN B 55 GLN B 92 ASN B 373 ASN B 380 GLN C 223 ASN C 284 HIS D 314 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103417 restraints weight = 16527.601| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.95 r_work: 0.3083 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 12468 Z= 0.259 Angle : 0.646 8.002 16830 Z= 0.334 Chirality : 0.047 0.146 1880 Planarity : 0.004 0.046 2146 Dihedral : 6.919 70.716 1666 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.86 % Allowed : 16.34 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1482 helix: -0.43 (0.21), residues: 554 sheet: -1.11 (0.27), residues: 318 loop : -0.79 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 285 HIS 0.005 0.001 HIS B 463 PHE 0.022 0.002 PHE C 344 TYR 0.023 0.002 TYR D 230 ARG 0.007 0.001 ARG B 663 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 513) hydrogen bonds : angle 5.17361 ( 1488) covalent geometry : bond 0.00619 (12468) covalent geometry : angle 0.64575 (16830) *********************** 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 201 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8414 (mttt) REVERT: A 349 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7604 (pp20) REVERT: A 447 VAL cc_start: 0.7992 (m) cc_final: 0.7787 (t) REVERT: A 653 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8487 (p) REVERT: B 11 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: B 76 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: B 268 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7772 (mptp) REVERT: B 279 ASP cc_start: 0.7560 (p0) cc_final: 0.7248 (p0) REVERT: B 312 GLU cc_start: 0.7612 (tt0) cc_final: 0.7361 (tt0) REVERT: B 385 MET cc_start: 0.8257 (mmp) cc_final: 0.8014 (mmm) REVERT: B 408 GLU cc_start: 0.8345 (tp30) cc_final: 0.8140 (tp30) REVERT: B 448 ASP cc_start: 0.8442 (p0) cc_final: 0.8241 (p0) REVERT: B 513 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: B 535 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 548 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8412 (ptpt) REVERT: C 212 ASN cc_start: 0.8294 (m-40) cc_final: 0.8054 (m110) REVERT: C 258 LYS cc_start: 0.7977 (mtpm) cc_final: 0.7742 (mmtp) REVERT: D 247 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: D 311 THR cc_start: 0.8806 (m) cc_final: 0.8605 (m) outliers start: 52 outliers final: 11 residues processed: 191 average time/residue: 1.4433 time to fit residues: 296.7470 Evaluate side-chains 138 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 586 GLU 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 349 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 29 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN B 197 HIS C 212 ASN C 223 ASN C 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107435 restraints weight = 16405.254| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.93 r_work: 0.3144 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12468 Z= 0.111 Angle : 0.487 5.825 16830 Z= 0.255 Chirality : 0.042 0.145 1880 Planarity : 0.003 0.044 2146 Dihedral : 6.407 69.170 1666 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.27 % Allowed : 16.86 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1482 helix: 0.11 (0.22), residues: 574 sheet: -1.10 (0.27), residues: 318 loop : -0.74 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.002 0.001 HIS B 463 PHE 0.014 0.001 PHE B 6 TYR 0.017 0.001 TYR D 230 ARG 0.003 0.000 ARG B 663 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 513) hydrogen bonds : angle 4.74289 ( 1488) covalent geometry : bond 0.00259 (12468) covalent geometry : angle 0.48699 (16830) *********************** 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 179 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 338 LYS cc_start: 0.9266 (mttm) cc_final: 0.9066 (mttt) REVERT: A 349 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7715 (pp20) REVERT: A 384 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7915 (tp) REVERT: A 447 VAL cc_start: 0.7949 (m) cc_final: 0.7718 (t) REVERT: A 544 GLU cc_start: 0.8088 (tp30) cc_final: 0.7831 (tp30) REVERT: A 606 LYS cc_start: 0.4503 (pmmt) cc_final: 0.3798 (ptpp) REVERT: A 633 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8340 (tptp) REVERT: A 653 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8423 (p) REVERT: B 76 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: B 268 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7802 (mptp) REVERT: B 312 GLU cc_start: 0.7498 (tt0) cc_final: 0.7217 (tt0) REVERT: B 398 GLU cc_start: 0.8211 (tp30) cc_final: 0.7917 (mm-30) REVERT: B 408 GLU cc_start: 0.8361 (tp30) cc_final: 0.8156 (tp30) REVERT: B 448 ASP cc_start: 0.8470 (p0) cc_final: 0.8260 (p0) REVERT: B 535 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 548 LYS cc_start: 0.8689 (ptpt) cc_final: 0.8448 (mtmm) REVERT: B 606 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7339 (mppt) REVERT: C 316 LYS cc_start: 0.8332 (tptt) cc_final: 0.8050 (mmmt) REVERT: D 247 GLN cc_start: 0.8595 (mt0) cc_final: 0.8359 (tt0) REVERT: D 316 LYS cc_start: 0.8225 (tptt) cc_final: 0.7917 (mmmt) outliers start: 44 outliers final: 12 residues processed: 171 average time/residue: 1.5255 time to fit residues: 280.8727 Evaluate side-chains 143 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 76 GLU 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 C residue 218 LEU Chi-restraints excluded: chain C residue 245 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 245 SER 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 110 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 112 optimal weight: 0.0770 chunk 132 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105568 restraints weight = 16485.044| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.90 r_work: 0.3116 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12468 Z= 0.149 Angle : 0.510 5.894 16830 Z= 0.266 Chirality : 0.042 0.141 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.492 68.074 1666 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.42 % Allowed : 17.24 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1482 helix: 0.53 (0.22), residues: 558 sheet: -1.13 (0.27), residues: 306 loop : -0.70 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.003 0.001 HIS B 463 PHE 0.013 0.002 PHE B 6 TYR 0.014 0.001 TYR D 230 ARG 0.004 0.000 ARG B 663 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 513) hydrogen bonds : angle 4.68545 ( 1488) covalent geometry : bond 0.00355 (12468) covalent geometry : angle 0.51016 (16830) *********************** 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 177 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7753 (pp20) REVERT: A 384 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8092 (tp) REVERT: A 386 LYS cc_start: 0.8485 (mmmt) cc_final: 0.7990 (mtmt) REVERT: A 447 VAL cc_start: 0.8023 (m) cc_final: 0.7791 (t) REVERT: A 653 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 666 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7155 (ttm-80) REVERT: B 76 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: B 268 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7798 (mptp) REVERT: B 312 GLU cc_start: 0.7563 (tt0) cc_final: 0.7292 (tt0) REVERT: B 398 GLU cc_start: 0.8202 (tp30) cc_final: 0.7904 (mm-30) REVERT: B 448 ASP cc_start: 0.8474 (p0) cc_final: 0.8253 (p0) REVERT: B 535 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 538 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8023 (mtpm) REVERT: B 548 LYS cc_start: 0.8646 (ptpt) cc_final: 0.8370 (mtmm) REVERT: B 606 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7456 (mppt) REVERT: C 247 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8304 (tp-100) REVERT: C 258 LYS cc_start: 0.7951 (mtpm) cc_final: 0.7733 (mmtp) REVERT: C 316 LYS cc_start: 0.8298 (tptt) cc_final: 0.8009 (mmmt) REVERT: D 247 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: D 278 ASP cc_start: 0.8275 (m-30) cc_final: 0.8073 (m-30) REVERT: D 316 LYS cc_start: 0.8242 (tptt) cc_final: 0.7908 (mmmt) outliers start: 46 outliers final: 14 residues processed: 165 average time/residue: 1.4655 time to fit residues: 260.3047 Evaluate side-chains 143 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 666 ARG Chi-restraints excluded: chain B residue 76 GLU 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 538 LYS Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 569 ASP 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 257 THR Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain D residue 218 LEU 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 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 373 ASN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107191 restraints weight = 16686.250| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.93 r_work: 0.3143 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12468 Z= 0.108 Angle : 0.471 5.417 16830 Z= 0.246 Chirality : 0.041 0.137 1880 Planarity : 0.003 0.042 2146 Dihedral : 6.268 70.195 1666 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.30 % Allowed : 18.95 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1482 helix: 0.62 (0.22), residues: 580 sheet: -1.00 (0.26), residues: 338 loop : -0.67 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.002 0.001 HIS B 463 PHE 0.013 0.001 PHE B 6 TYR 0.014 0.001 TYR D 230 ARG 0.003 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 513) hydrogen bonds : angle 4.52086 ( 1488) covalent geometry : bond 0.00255 (12468) covalent geometry : angle 0.47065 (16830) *********************** 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 171 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7808 (pp20) REVERT: A 383 LYS cc_start: 0.6967 (pttt) cc_final: 0.6636 (tptt) REVERT: A 398 GLU cc_start: 0.8283 (tp30) cc_final: 0.8013 (mm-30) REVERT: A 447 VAL cc_start: 0.7992 (m) cc_final: 0.7784 (t) REVERT: A 606 LYS cc_start: 0.4577 (pmmt) cc_final: 0.3845 (ptpp) REVERT: A 653 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 666 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7122 (ttm-80) REVERT: B 268 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7809 (mptp) REVERT: B 312 GLU cc_start: 0.7532 (tt0) cc_final: 0.7202 (tt0) REVERT: B 398 GLU cc_start: 0.8201 (tp30) cc_final: 0.7912 (mm-30) REVERT: B 448 ASP cc_start: 0.8495 (p0) cc_final: 0.8271 (p0) REVERT: B 535 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 548 LYS cc_start: 0.8629 (ptpt) cc_final: 0.8118 (ttpp) REVERT: B 606 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7423 (mppt) REVERT: B 637 ASP cc_start: 0.8374 (m-30) cc_final: 0.8147 (m-30) REVERT: C 247 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8300 (tp-100) REVERT: C 258 LYS cc_start: 0.7893 (mtpm) cc_final: 0.7680 (mmtp) REVERT: C 316 LYS cc_start: 0.8330 (tptt) cc_final: 0.8081 (mmmt) REVERT: D 247 GLN cc_start: 0.8563 (mt0) cc_final: 0.8253 (tt0) REVERT: D 316 LYS cc_start: 0.8138 (tptt) cc_final: 0.7861 (mmmt) outliers start: 31 outliers final: 14 residues processed: 161 average time/residue: 1.5049 time to fit residues: 261.1347 Evaluate side-chains 142 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 666 ARG Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 569 ASP 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 218 LEU 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 145 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN B 373 ASN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106739 restraints weight = 16515.930| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.93 r_work: 0.3136 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12468 Z= 0.116 Angle : 0.487 6.305 16830 Z= 0.254 Chirality : 0.041 0.136 1880 Planarity : 0.003 0.042 2146 Dihedral : 6.243 68.941 1666 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.82 % Allowed : 18.72 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1482 helix: 0.72 (0.22), residues: 582 sheet: -0.95 (0.26), residues: 338 loop : -0.62 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 148 HIS 0.002 0.001 HIS B 463 PHE 0.013 0.001 PHE B 6 TYR 0.025 0.001 TYR D 230 ARG 0.002 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 513) hydrogen bonds : angle 4.48808 ( 1488) covalent geometry : bond 0.00274 (12468) covalent geometry : angle 0.48710 (16830) *********************** 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 169 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: A 178 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8287 (mttt) REVERT: A 349 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7789 (pp20) REVERT: A 386 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7926 (mtpt) REVERT: A 398 GLU cc_start: 0.8289 (tp30) cc_final: 0.8020 (mm-30) REVERT: A 606 LYS cc_start: 0.4619 (pmmt) cc_final: 0.3852 (ptpp) REVERT: A 636 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7625 (mtpp) REVERT: A 653 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 666 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7093 (ttm-80) REVERT: B 268 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7826 (mptp) REVERT: B 312 GLU cc_start: 0.7544 (tt0) cc_final: 0.7221 (tt0) REVERT: B 398 GLU cc_start: 0.8202 (tp30) cc_final: 0.7920 (mm-30) REVERT: B 535 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 538 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8090 (mtpp) REVERT: B 606 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7456 (mppt) REVERT: B 637 ASP cc_start: 0.8440 (m-30) cc_final: 0.8201 (m-30) REVERT: C 247 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8313 (tp-100) REVERT: C 258 LYS cc_start: 0.7918 (mtpm) cc_final: 0.7693 (mmtp) REVERT: C 311 THR cc_start: 0.8947 (t) cc_final: 0.8702 (t) REVERT: C 316 LYS cc_start: 0.8301 (tptt) cc_final: 0.8054 (mmmt) REVERT: D 247 GLN cc_start: 0.8596 (mt0) cc_final: 0.8392 (tt0) REVERT: D 316 LYS cc_start: 0.8124 (tptt) cc_final: 0.7841 (mmmt) outliers start: 38 outliers final: 17 residues processed: 158 average time/residue: 1.4484 time to fit residues: 246.9401 Evaluate side-chains 147 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 262 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 623 LYS 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 407 SER Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 556 ASP 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 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 116 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN C 223 ASN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109878 restraints weight = 16661.659| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.92 r_work: 0.3182 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12468 Z= 0.086 Angle : 0.459 6.451 16830 Z= 0.238 Chirality : 0.041 0.136 1880 Planarity : 0.003 0.042 2146 Dihedral : 5.995 69.414 1666 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1482 helix: 0.91 (0.23), residues: 582 sheet: -0.74 (0.27), residues: 334 loop : -0.56 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.001 0.000 HIS B 463 PHE 0.013 0.001 PHE B 6 TYR 0.024 0.001 TYR C 230 ARG 0.002 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.02639 ( 513) hydrogen bonds : angle 4.33675 ( 1488) covalent geometry : bond 0.00196 (12468) covalent geometry : angle 0.45858 (16830) *********************** 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 168 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.849 Fit side-chains revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 349 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7724 (pp20) REVERT: A 386 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7849 (mtmt) REVERT: A 398 GLU cc_start: 0.8208 (tp30) cc_final: 0.7973 (mm-30) REVERT: A 606 LYS cc_start: 0.4510 (pmmt) cc_final: 0.3757 (ptpp) REVERT: B 268 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7807 (mptp) REVERT: B 312 GLU cc_start: 0.7462 (tt0) cc_final: 0.7261 (tt0) REVERT: B 398 GLU cc_start: 0.8129 (tp30) cc_final: 0.7875 (mm-30) REVERT: B 502 ASP cc_start: 0.8888 (m-30) cc_final: 0.8643 (m-30) REVERT: B 535 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 538 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8075 (mtpp) REVERT: B 548 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8134 (ttpp) REVERT: B 606 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7381 (mppt) REVERT: B 637 ASP cc_start: 0.8442 (m-30) cc_final: 0.8210 (m-30) REVERT: C 247 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: C 311 THR cc_start: 0.8898 (t) cc_final: 0.8682 (t) REVERT: C 316 LYS cc_start: 0.8275 (tptt) cc_final: 0.8072 (mmmt) REVERT: D 247 GLN cc_start: 0.8554 (mt0) cc_final: 0.8352 (tt0) REVERT: D 316 LYS cc_start: 0.8084 (tptt) cc_final: 0.7808 (mmmt) outliers start: 26 outliers final: 14 residues processed: 162 average time/residue: 1.5073 time to fit residues: 265.6740 Evaluate side-chains 145 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 311 LEU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 621 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 538 LYS Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 569 ASP 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 274 SER Chi-restraints excluded: chain D residue 245 SER 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 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 78 optimal weight: 0.0000 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN C 223 ASN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106862 restraints weight = 16922.130| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.84 r_work: 0.3139 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12468 Z= 0.120 Angle : 0.498 7.894 16830 Z= 0.258 Chirality : 0.042 0.136 1880 Planarity : 0.003 0.042 2146 Dihedral : 6.178 68.337 1666 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.01 % Allowed : 20.13 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1482 helix: 0.91 (0.23), residues: 580 sheet: -0.82 (0.27), residues: 328 loop : -0.53 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 148 HIS 0.002 0.001 HIS B 463 PHE 0.012 0.001 PHE B 6 TYR 0.025 0.001 TYR C 230 ARG 0.003 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 513) hydrogen bonds : angle 4.41553 ( 1488) covalent geometry : bond 0.00286 (12468) covalent geometry : angle 0.49848 (16830) *********************** 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 155 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: A 349 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7703 (pp20) REVERT: A 386 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7908 (mtpt) REVERT: A 398 GLU cc_start: 0.8223 (tp30) cc_final: 0.7968 (mm-30) REVERT: A 606 LYS cc_start: 0.4606 (pmmt) cc_final: 0.3810 (ptpp) REVERT: B 268 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7791 (mptp) REVERT: B 398 GLU cc_start: 0.8135 (tp30) cc_final: 0.7876 (mm-30) REVERT: B 535 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 538 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8058 (mtpp) REVERT: B 548 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8219 (ttpp) REVERT: B 606 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7494 (mppt) REVERT: B 637 ASP cc_start: 0.8487 (m-30) cc_final: 0.8220 (m-30) REVERT: C 247 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: C 311 THR cc_start: 0.8864 (t) cc_final: 0.8634 (t) REVERT: C 316 LYS cc_start: 0.8220 (tptt) cc_final: 0.7948 (mmmt) REVERT: D 247 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: D 316 LYS cc_start: 0.8113 (tptt) cc_final: 0.7819 (mmmt) outliers start: 27 outliers final: 14 residues processed: 149 average time/residue: 1.3552 time to fit residues: 219.0238 Evaluate side-chains 143 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 311 LEU Chi-restraints excluded: chain A residue 556 ASP 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 538 LYS Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 569 ASP 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 349 VAL 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 14 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN B 373 ASN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106604 restraints weight = 16837.533| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.82 r_work: 0.3138 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12468 Z= 0.121 Angle : 0.496 7.678 16830 Z= 0.257 Chirality : 0.042 0.136 1880 Planarity : 0.003 0.042 2146 Dihedral : 6.226 68.920 1666 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.56 % Allowed : 20.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1482 helix: 0.89 (0.22), residues: 580 sheet: -0.82 (0.27), residues: 328 loop : -0.58 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.002 0.001 HIS B 463 PHE 0.012 0.001 PHE B 6 TYR 0.025 0.001 TYR C 230 ARG 0.002 0.000 ARG B 663 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 513) hydrogen bonds : angle 4.44302 ( 1488) covalent geometry : bond 0.00289 (12468) covalent geometry : angle 0.49584 (16830) ********************** 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 150 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: A 349 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7718 (pp20) REVERT: A 386 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7913 (mtpt) REVERT: A 398 GLU cc_start: 0.8237 (tp30) cc_final: 0.7980 (mm-30) REVERT: A 606 LYS cc_start: 0.4701 (pmmt) cc_final: 0.3881 (ptpp) REVERT: A 636 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7696 (mtpp) REVERT: B 268 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7790 (mptp) REVERT: B 398 GLU cc_start: 0.8140 (tp30) cc_final: 0.7876 (mm-30) REVERT: B 502 ASP cc_start: 0.8901 (m-30) cc_final: 0.8668 (m-30) REVERT: B 535 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 538 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8247 (mtpm) REVERT: B 548 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8170 (ttpp) REVERT: B 606 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7486 (mppt) REVERT: B 637 ASP cc_start: 0.8504 (m-30) cc_final: 0.8237 (m-30) REVERT: C 247 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 311 THR cc_start: 0.8870 (t) cc_final: 0.8643 (t) REVERT: C 316 LYS cc_start: 0.8237 (tptt) cc_final: 0.7958 (mmmt) REVERT: D 247 GLN cc_start: 0.8590 (mt0) cc_final: 0.8387 (tt0) REVERT: D 316 LYS cc_start: 0.8127 (tptt) cc_final: 0.7845 (mmmt) outliers start: 21 outliers final: 12 residues processed: 147 average time/residue: 1.3441 time to fit residues: 214.3218 Evaluate side-chains 138 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 311 LEU Chi-restraints excluded: chain A residue 465 LYS 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 538 LYS Chi-restraints excluded: chain B residue 556 ASP 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 D residue 245 SER 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 101 optimal weight: 4.9990 chunk 131 optimal weight: 0.0870 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 0.0040 chunk 22 optimal weight: 0.8980 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN B 381 GLN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108694 restraints weight = 16520.226| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.92 r_work: 0.3166 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12468 Z= 0.097 Angle : 0.473 7.908 16830 Z= 0.246 Chirality : 0.041 0.135 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.071 69.372 1666 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.26 % Allowed : 20.73 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1482 helix: 0.96 (0.22), residues: 582 sheet: -0.72 (0.27), residues: 326 loop : -0.57 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.002 0.001 HIS D 303 PHE 0.012 0.001 PHE B 6 TYR 0.024 0.001 TYR C 230 ARG 0.002 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.02756 ( 513) hydrogen bonds : angle 4.35151 ( 1488) covalent geometry : bond 0.00225 (12468) covalent geometry : angle 0.47320 (16830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9629.66 seconds wall clock time: 167 minutes 6.00 seconds (10026.00 seconds total)