Starting phenix.real_space_refine on Thu Sep 26 06:32:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/09_2024/6xle_22241.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/09_2024/6xle_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/09_2024/6xle_22241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/09_2024/6xle_22241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/09_2024/6xle_22241.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/09_2024/6xle_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-5461/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: 7.65, per 1000 atoms: 0.62 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: 2.90 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: 1.62 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: 3.92 Time building geometry restraints manager: 3.38 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: 0.00 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: 0.890 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.360 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- 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= 0.216 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 357 time to evaluate : 1.381 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 1.6829 time to fit residues: 640.3925 Evaluate side-chains 162 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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= 0.193 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 *********************** 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 fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: B 14 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7338 (tm-30) REVERT: B 268 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7467 (mptp) REVERT: D 247 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: D 331 ASN cc_start: 0.8968 (m110) cc_final: 0.8767 (m110) outliers start: 37 outliers final: 12 residues processed: 204 average time/residue: 1.3202 time to fit residues: 291.4776 Evaluate side-chains 146 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 74 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 92 ASN B 373 ASN B 380 GLN C 223 ASN D 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12468 Z= 0.285 Angle : 0.578 7.826 16830 Z= 0.299 Chirality : 0.044 0.143 1880 Planarity : 0.004 0.043 2146 Dihedral : 6.586 68.978 1666 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.49 % Allowed : 16.72 % 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: -1.13 (0.21), residues: 1482 helix: -0.32 (0.21), residues: 552 sheet: -1.09 (0.27), residues: 318 loop : -0.76 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 285 HIS 0.004 0.001 HIS B 197 PHE 0.018 0.002 PHE C 344 TYR 0.022 0.002 TYR D 230 ARG 0.004 0.001 ARG B 663 *********************** 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 191 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 144 time to evaluate : 1.417 Fit side-chains REVERT: A 653 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8212 (p) REVERT: B 11 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: B 268 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7625 (mptp) REVERT: B 385 MET cc_start: 0.7705 (mmp) cc_final: 0.7406 (mmm) REVERT: B 513 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6380 (pt0) REVERT: B 548 LYS cc_start: 0.8409 (ptpt) cc_final: 0.8135 (ptpt) REVERT: C 212 ASN cc_start: 0.8143 (m-40) cc_final: 0.7919 (m110) REVERT: D 247 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7797 (tt0) outliers start: 47 outliers final: 11 residues processed: 183 average time/residue: 1.3204 time to fit residues: 261.4287 Evaluate side-chains 133 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 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 B residue 623 LYS Chi-restraints excluded: chain C residue 245 SER 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 Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN A 466 ASN B 197 HIS C 223 ASN C 331 ASN D 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12468 Z= 0.166 Angle : 0.481 6.041 16830 Z= 0.251 Chirality : 0.042 0.143 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.266 67.484 1666 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.67 % Allowed : 17.16 % Favored : 80.16 % 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: -0.80 (0.21), residues: 1482 helix: 0.13 (0.22), residues: 574 sheet: -1.03 (0.27), residues: 318 loop : -0.70 (0.24), residues: 590 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 0.023 0.001 TYR C 230 ARG 0.003 0.000 ARG A 575 *********************** 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 168 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: B 268 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7706 (mptp) REVERT: B 308 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6667 (mm-30) REVERT: B 548 LYS cc_start: 0.8374 (ptpt) cc_final: 0.8147 (mtmm) REVERT: C 212 ASN cc_start: 0.8139 (m-40) cc_final: 0.7911 (m110) REVERT: C 316 LYS cc_start: 0.7915 (tptt) cc_final: 0.7703 (mmmt) REVERT: D 238 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7446 (ttp-170) REVERT: D 247 GLN cc_start: 0.8036 (mt0) cc_final: 0.7828 (tt0) REVERT: D 316 LYS cc_start: 0.7928 (tptt) cc_final: 0.7687 (mmmt) outliers start: 36 outliers final: 12 residues processed: 158 average time/residue: 1.3641 time to fit residues: 233.2798 Evaluate side-chains 137 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 308 GLU 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 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN C 223 ASN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12468 Z= 0.321 Angle : 0.568 7.135 16830 Z= 0.295 Chirality : 0.045 0.142 1880 Planarity : 0.004 0.044 2146 Dihedral : 6.737 69.711 1666 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.97 % Allowed : 17.76 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.66 (0.21), residues: 1482 helix: 0.40 (0.22), residues: 558 sheet: -1.10 (0.27), residues: 306 loop : -0.70 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 285 HIS 0.004 0.001 HIS B 463 PHE 0.017 0.002 PHE C 344 TYR 0.024 0.002 TYR C 230 ARG 0.006 0.001 ARG B 595 *********************** 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 167 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 384 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7759 (tp) REVERT: A 606 LYS cc_start: 0.4630 (pmtt) cc_final: 0.4269 (pmtt) REVERT: A 653 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8391 (p) REVERT: A 666 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.7015 (ttm-80) REVERT: B 268 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7685 (mptp) REVERT: B 308 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: B 548 LYS cc_start: 0.8345 (ptpt) cc_final: 0.8120 (mtmm) REVERT: D 238 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7407 (ttp-170) REVERT: D 247 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: D 316 LYS cc_start: 0.7955 (tptt) cc_final: 0.7672 (mmmt) outliers start: 40 outliers final: 15 residues processed: 159 average time/residue: 1.4955 time to fit residues: 255.5731 Evaluate side-chains 137 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 384 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 635 VAL 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 291 SER Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 384 ILE 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 257 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN A 592 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12468 Z= 0.214 Angle : 0.510 6.033 16830 Z= 0.266 Chirality : 0.042 0.139 1880 Planarity : 0.003 0.044 2146 Dihedral : 6.522 68.531 1666 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.53 % Allowed : 18.28 % Favored : 79.20 % 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: -0.49 (0.21), residues: 1482 helix: 0.62 (0.23), residues: 558 sheet: -1.08 (0.28), residues: 306 loop : -0.65 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.003 0.001 HIS B 463 PHE 0.014 0.001 PHE B 6 TYR 0.020 0.002 TYR C 230 ARG 0.003 0.000 ARG B 663 *********************** 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 160 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7661 (mtpp) REVERT: A 653 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8420 (p) REVERT: A 666 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6973 (ttm-80) REVERT: B 268 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7697 (mptp) REVERT: B 308 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: B 548 LYS cc_start: 0.8340 (ptpt) cc_final: 0.8138 (mtmm) REVERT: C 247 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7921 (tp-100) REVERT: D 238 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7423 (ttp-170) REVERT: D 316 LYS cc_start: 0.7961 (tptt) cc_final: 0.7692 (mmmt) outliers start: 34 outliers final: 12 residues processed: 149 average time/residue: 1.4309 time to fit residues: 228.9222 Evaluate side-chains 134 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 208 LEU 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 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 0.2980 chunk 104 optimal weight: 0.0040 chunk 120 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 86 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.3430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN D 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12468 Z= 0.128 Angle : 0.466 6.689 16830 Z= 0.244 Chirality : 0.041 0.136 1880 Planarity : 0.003 0.044 2146 Dihedral : 6.107 71.013 1666 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.78 % Allowed : 19.32 % Favored : 78.90 % 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: -0.32 (0.21), residues: 1482 helix: 0.75 (0.23), residues: 582 sheet: -0.86 (0.27), residues: 322 loop : -0.66 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 148 HIS 0.002 0.000 HIS B 463 PHE 0.013 0.001 PHE B 6 TYR 0.020 0.001 TYR C 230 ARG 0.002 0.000 ARG A 575 *********************** 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 167 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 636 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7703 (mtpp) REVERT: A 666 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6901 (ttm-80) REVERT: B 11 GLU cc_start: 0.7271 (tt0) cc_final: 0.6862 (tt0) REVERT: B 502 ASP cc_start: 0.8386 (m-30) cc_final: 0.8163 (m-30) REVERT: C 247 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7901 (tp-100) REVERT: C 311 THR cc_start: 0.8809 (t) cc_final: 0.8601 (t) REVERT: C 316 LYS cc_start: 0.7882 (tptt) cc_final: 0.7656 (mmmt) REVERT: D 238 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7460 (ttp-170) REVERT: D 316 LYS cc_start: 0.7841 (tptt) cc_final: 0.7550 (mmmt) outliers start: 24 outliers final: 10 residues processed: 162 average time/residue: 1.2451 time to fit residues: 217.3181 Evaluate side-chains 131 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 291 SER 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 556 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.0370 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12468 Z= 0.222 Angle : 0.533 7.516 16830 Z= 0.275 Chirality : 0.043 0.136 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.386 68.076 1666 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.56 % Allowed : 20.06 % 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: -0.26 (0.21), residues: 1482 helix: 0.89 (0.23), residues: 558 sheet: -0.96 (0.27), residues: 328 loop : -0.59 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 285 HIS 0.003 0.001 HIS B 463 PHE 0.014 0.001 PHE A 410 TYR 0.024 0.002 TYR C 230 ARG 0.003 0.000 ARG B 376 *********************** 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 142 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.406 Fit side-chains revert: symmetry clash REVERT: A 636 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7736 (mtpp) REVERT: B 268 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7713 (mptp) REVERT: B 385 MET cc_start: 0.7777 (mmp) cc_final: 0.7493 (mmm) REVERT: B 548 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8045 (ttpp) REVERT: C 247 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7917 (tp-100) REVERT: C 311 THR cc_start: 0.8826 (t) cc_final: 0.8625 (t) REVERT: C 316 LYS cc_start: 0.7948 (tptt) cc_final: 0.7731 (mmmt) REVERT: D 238 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7489 (ttp-170) REVERT: D 316 LYS cc_start: 0.7871 (tptt) cc_final: 0.7632 (mmmt) outliers start: 21 outliers final: 10 residues processed: 135 average time/residue: 1.2912 time to fit residues: 189.6405 Evaluate side-chains 126 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 238 ARG 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 136 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12468 Z= 0.228 Angle : 0.535 7.221 16830 Z= 0.276 Chirality : 0.043 0.135 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.475 68.580 1666 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.49 % Allowed : 20.28 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.21), residues: 1482 helix: 0.89 (0.23), residues: 558 sheet: -0.94 (0.27), residues: 328 loop : -0.64 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 148 HIS 0.003 0.001 HIS B 463 PHE 0.013 0.001 PHE B 6 TYR 0.024 0.002 TYR C 230 ARG 0.003 0.000 ARG B 663 *********************** 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 140 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 636 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7746 (mtpp) REVERT: A 653 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8390 (p) REVERT: B 268 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7729 (mptp) REVERT: B 548 LYS cc_start: 0.8288 (mtmm) cc_final: 0.8037 (ttpp) REVERT: C 247 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7926 (tp-100) REVERT: C 311 THR cc_start: 0.8820 (t) cc_final: 0.8619 (t) REVERT: C 316 LYS cc_start: 0.7897 (tptt) cc_final: 0.7670 (mmmt) REVERT: D 238 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7448 (ttp-170) REVERT: D 316 LYS cc_start: 0.7863 (tptt) cc_final: 0.7571 (mmmt) outliers start: 20 outliers final: 9 residues processed: 134 average time/residue: 1.3459 time to fit residues: 195.6642 Evaluate side-chains 123 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 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 349 VAL Chi-restraints excluded: chain D residue 238 ARG 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 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12468 Z= 0.238 Angle : 0.549 7.230 16830 Z= 0.284 Chirality : 0.043 0.136 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.520 68.149 1666 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.34 % Allowed : 20.58 % Favored : 78.08 % 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: -0.27 (0.21), residues: 1482 helix: 0.89 (0.23), residues: 558 sheet: -0.90 (0.27), residues: 328 loop : -0.65 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.004 0.001 HIS D 303 PHE 0.013 0.001 PHE A 410 TYR 0.024 0.002 TYR C 230 ARG 0.003 0.000 ARG B 376 ********************** 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 129 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.306 Fit side-chains REVERT: A 636 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7760 (mtpp) REVERT: A 653 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8409 (p) REVERT: B 268 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7737 (mptp) REVERT: C 247 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7934 (tp-100) REVERT: C 316 LYS cc_start: 0.7903 (tptt) cc_final: 0.7670 (mmmt) REVERT: D 238 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7439 (ttp-170) REVERT: D 316 LYS cc_start: 0.7880 (tptt) cc_final: 0.7594 (mmmt) outliers start: 18 outliers final: 10 residues processed: 125 average time/residue: 1.2887 time to fit residues: 175.2530 Evaluate side-chains 123 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 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 238 ARG 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 35 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 120 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 0.0470 chunk 6 optimal weight: 0.0980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 GLN C 314 GLN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108970 restraints weight = 16454.802| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.90 r_work: 0.3168 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12468 Z= 0.135 Angle : 0.492 7.708 16830 Z= 0.254 Chirality : 0.041 0.135 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.156 70.208 1666 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.04 % Allowed : 20.65 % 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: -0.15 (0.21), residues: 1482 helix: 0.90 (0.23), residues: 576 sheet: -0.76 (0.28), residues: 320 loop : -0.58 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 148 HIS 0.003 0.001 HIS D 303 PHE 0.013 0.001 PHE B 6 TYR 0.024 0.001 TYR C 230 ARG 0.002 0.000 ARG A 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4627.35 seconds wall clock time: 81 minutes 36.55 seconds (4896.55 seconds total)