Starting phenix.real_space_refine on Wed Aug 5 09:24:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9och_70315/08_2026/9och_70315.cif Found real_map, /net/cci-nas-00/data/ceres_data/9och_70315/08_2026/9och_70315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9och_70315/08_2026/9och_70315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9och_70315/08_2026/9och_70315.map" model { file = "/net/cci-nas-00/data/ceres_data/9och_70315/08_2026/9och_70315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9och_70315/08_2026/9och_70315.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 5642 2.51 5 N 1545 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4288 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 20, 'TRANS': 527} Chain: "D" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 279 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "A" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4268 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 21, 'TRANS': 529} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.98, per 1000 atoms: 0.22 Number of scatterers: 8895 At special positions: 0 Unit cell: (73.08, 90.48, 141.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 5 15.00 Mg 2 11.99 O 1657 8.00 N 1545 7.00 C 5642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 325.8 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 69.0% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 134 through 146 removed outlier: 3.703A pdb=" N MET B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.798A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 234 removed outlier: 3.601A pdb=" N SER B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS B 213 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.504A pdb=" N GLU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 262 removed outlier: 4.569A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 284 removed outlier: 4.879A pdb=" N ASN B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 288 through 338 removed outlier: 4.198A pdb=" N LEU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 300 " --> pdb=" O SER B 296 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.639A pdb=" N ALA B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 399 removed outlier: 3.619A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 440 removed outlier: 3.643A pdb=" N LEU B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 4.172A pdb=" N PHE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 517 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.519A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.675A pdb=" N GLN B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.523A pdb=" N GLN B 667 " --> pdb=" O GLN B 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 129 through 135 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 185 through 203 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.848A pdb=" N PHE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 269 removed outlier: 4.065A pdb=" N MET A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.560A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 324 removed outlier: 3.703A pdb=" N SER A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 373 removed outlier: 5.065A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 434 removed outlier: 3.724A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 475 removed outlier: 3.830A pdb=" N PHE A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 456 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.560A pdb=" N ILE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.551A pdb=" N SER A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 644 through 658 removed outlier: 3.753A pdb=" N ARG A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 649 " --> pdb=" O GLY A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.980A pdb=" N TYR A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 693 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 removed outlier: 3.856A pdb=" N LYS A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.685A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 468 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.685A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.364A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 7.828A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.731A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE A 699 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 666 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 711 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1623 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: 1.24 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2612 1.34 - 1.46: 1405 1.46 - 1.58: 4962 1.58 - 1.70: 8 1.70 - 1.82: 71 Bond restraints: 9058 Sorted by residual: bond pdb=" CA PHE B 302 " pdb=" C PHE B 302 " ideal model delta sigma weight residual 1.524 1.573 -0.049 1.24e-02 6.50e+03 1.58e+01 bond pdb=" CA MET D 124 " pdb=" C MET D 124 " ideal model delta sigma weight residual 1.522 1.564 -0.042 1.39e-02 5.18e+03 9.21e+00 bond pdb=" N PHE B 158 " pdb=" CA PHE B 158 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" CA PHE B 157 " pdb=" C PHE B 157 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.32e-02 5.74e+03 3.71e+00 bond pdb=" C ARG B 494 " pdb=" N PRO B 495 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.32e-02 5.74e+03 3.06e+00 ... (remaining 9053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12087 2.29 - 4.57: 159 4.57 - 6.86: 35 6.86 - 9.15: 8 9.15 - 11.43: 2 Bond angle restraints: 12291 Sorted by residual: angle pdb=" N THR B 303 " pdb=" CA THR B 303 " pdb=" C THR B 303 " ideal model delta sigma weight residual 111.28 122.71 -11.43 1.09e+00 8.42e-01 1.10e+02 angle pdb=" C ASN D 125 " pdb=" CA ASN D 125 " pdb=" CB ASN D 125 " ideal model delta sigma weight residual 117.23 109.79 7.44 1.36e+00 5.41e-01 2.99e+01 angle pdb=" N ASN B 436 " pdb=" CA ASN B 436 " pdb=" C ASN B 436 " ideal model delta sigma weight residual 111.07 105.59 5.48 1.07e+00 8.73e-01 2.62e+01 angle pdb=" N PHE B 302 " pdb=" CA PHE B 302 " pdb=" C PHE B 302 " ideal model delta sigma weight residual 110.97 116.45 -5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" N THR B 303 " pdb=" CA THR B 303 " pdb=" CB THR B 303 " ideal model delta sigma weight residual 110.12 102.77 7.35 1.47e+00 4.63e-01 2.50e+01 ... (remaining 12286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4879 17.63 - 35.26: 436 35.26 - 52.89: 113 52.89 - 70.52: 22 70.52 - 88.15: 9 Dihedral angle restraints: 5459 sinusoidal: 2201 harmonic: 3258 Sorted by residual: dihedral pdb=" C PHE B 157 " pdb=" N PHE B 157 " pdb=" CA PHE B 157 " pdb=" CB PHE B 157 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA MET B 300 " pdb=" C MET B 300 " pdb=" N PRO B 301 " pdb=" CA PRO B 301 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" C PHE B 302 " pdb=" N PHE B 302 " pdb=" CA PHE B 302 " pdb=" CB PHE B 302 " ideal model delta harmonic sigma weight residual -122.60 -131.29 8.69 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1221 0.059 - 0.117: 182 0.117 - 0.176: 10 0.176 - 0.235: 7 0.235 - 0.293: 3 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CA PHE B 157 " pdb=" N PHE B 157 " pdb=" C PHE B 157 " pdb=" CB PHE B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA MET D 124 " pdb=" N MET D 124 " pdb=" C MET D 124 " pdb=" CB MET D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PHE B 302 " pdb=" N PHE B 302 " pdb=" C PHE B 302 " pdb=" CB PHE B 302 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1420 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 302 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C PHE B 302 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE B 302 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 303 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 428 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C TYR A 428 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR A 428 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 429 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 115 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 116 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 116 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 116 " 0.022 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 32 2.59 - 3.16: 7470 3.16 - 3.74: 13671 3.74 - 4.32: 17726 4.32 - 4.90: 30508 Nonbonded interactions: 69407 Sorted by model distance: nonbonded pdb=" O2B ADP B 701 " pdb="MG MG B 702 " model vdw 2.007 2.170 nonbonded pdb=" OG SER A 545 " pdb="MG MG A 902 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLN B 551 " pdb="MG MG B 702 " model vdw 2.029 2.170 nonbonded pdb=" O3G ATP A 901 " pdb="MG MG A 902 " model vdw 2.068 2.170 nonbonded pdb=" O2B ATP A 901 " pdb="MG MG A 902 " model vdw 2.201 2.170 ... (remaining 69402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.120 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 0.049 9058 Z= 0.150 Angle : 0.696 11.434 12291 Z= 0.401 Chirality : 0.045 0.293 1423 Planarity : 0.004 0.040 1569 Dihedral : 15.023 88.155 3365 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1124 helix: 1.36 (0.20), residues: 696 sheet: 0.89 (0.68), residues: 68 loop : 0.22 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.011 0.001 TYR B 415 PHE 0.023 0.002 PHE B 157 TRP 0.016 0.001 TRP A 413 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 ( 9058) covalent geometry : angle 0.69599 / 0.40 (12291) hydrogen bonds : bond 0.16610 / 11.38 ( 562) hydrogen bonds : angle 5.53722 / 4.08 ( 1623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: B 310 TYR cc_start: 0.8057 (t80) cc_final: 0.7371 (t80) REVERT: A 395 GLN cc_start: 0.7804 (tp40) cc_final: 0.7453 (tm-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0772 time to fit residues: 12.6693 Evaluate side-chains 106 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090419 restraints weight = 17573.520| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.10 r_work: 0.3090 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9058 Z= 0.126 Angle : 0.563 7.394 12291 Z= 0.279 Chirality : 0.039 0.131 1423 Planarity : 0.004 0.035 1569 Dihedral : 6.435 78.297 1275 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.45 % Allowed : 10.44 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1124 helix: 1.75 (0.20), residues: 705 sheet: 0.99 (0.69), residues: 68 loop : 0.25 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.012 0.001 TYR A 465 PHE 0.016 0.002 PHE B 157 TRP 0.007 0.001 TRP A 413 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 9058) covalent geometry : angle 0.56251 / 0.28 (12291) hydrogen bonds : bond 0.05235 / 3.51 ( 562) hydrogen bonds : angle 4.07289 / 2.92 ( 1623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: B 310 TYR cc_start: 0.8046 (t80) cc_final: 0.7263 (t80) REVERT: B 624 ASP cc_start: 0.8874 (t0) cc_final: 0.8672 (p0) REVERT: B 645 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8548 (mm) outliers start: 14 outliers final: 9 residues processed: 123 average time/residue: 0.0651 time to fit residues: 12.1261 Evaluate side-chains 119 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.110516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090656 restraints weight = 17452.725| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.10 r_work: 0.3091 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9058 Z= 0.114 Angle : 0.527 6.961 12291 Z= 0.258 Chirality : 0.038 0.127 1423 Planarity : 0.003 0.032 1569 Dihedral : 6.090 73.794 1275 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.55 % Allowed : 11.27 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.26), residues: 1124 helix: 2.10 (0.20), residues: 701 sheet: 0.86 (0.66), residues: 73 loop : 0.34 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.011 0.001 TYR A 465 PHE 0.011 0.001 PHE B 201 TRP 0.005 0.001 TRP A 413 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9058) covalent geometry : angle 0.52743 / 0.26 (12291) hydrogen bonds : bond 0.04778 / 3.21 ( 562) hydrogen bonds : angle 3.78447 / 2.73 ( 1623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: B 166 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7400 (mm-30) REVERT: B 285 MET cc_start: 0.8486 (tmm) cc_final: 0.8285 (tmm) REVERT: B 310 TYR cc_start: 0.7994 (t80) cc_final: 0.7235 (t80) REVERT: B 624 ASP cc_start: 0.8945 (t0) cc_final: 0.8579 (p0) REVERT: B 645 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 301 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8493 (mm-30) outliers start: 15 outliers final: 9 residues processed: 128 average time/residue: 0.0683 time to fit residues: 13.2026 Evaluate side-chains 116 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 98 optimal weight: 0.0770 chunk 96 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090168 restraints weight = 17656.401| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.13 r_work: 0.3086 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9058 Z= 0.118 Angle : 0.534 7.793 12291 Z= 0.259 Chirality : 0.038 0.154 1423 Planarity : 0.003 0.033 1569 Dihedral : 5.977 76.290 1275 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.76 % Allowed : 12.00 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.26), residues: 1124 helix: 2.13 (0.20), residues: 708 sheet: 0.84 (0.65), residues: 75 loop : 0.31 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.010 0.001 TYR A 465 PHE 0.011 0.001 PHE A 275 TRP 0.010 0.001 TRP B 263 HIS 0.002 0.001 HIS B 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9058) covalent geometry : angle 0.53429 / 0.26 (12291) hydrogen bonds : bond 0.04644 / 3.11 ( 562) hydrogen bonds : angle 3.71380 / 2.68 ( 1623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: B 285 MET cc_start: 0.8439 (tmm) cc_final: 0.8116 (tmm) REVERT: B 310 TYR cc_start: 0.8015 (t80) cc_final: 0.7321 (t80) REVERT: B 624 ASP cc_start: 0.8959 (t0) cc_final: 0.8566 (p0) REVERT: B 645 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 301 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8500 (mm-30) outliers start: 17 outliers final: 7 residues processed: 122 average time/residue: 0.0557 time to fit residues: 10.5308 Evaluate side-chains 111 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 333 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 93 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.5691 > 50:) chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.090356 restraints weight = 17606.994| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.11 r_work: 0.3092 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9058 Z= 0.116 Angle : 0.546 12.166 12291 Z= 0.261 Chirality : 0.038 0.196 1423 Planarity : 0.003 0.033 1569 Dihedral : 5.873 75.927 1275 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.17 % Allowed : 11.58 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.26), residues: 1124 helix: 2.16 (0.20), residues: 709 sheet: 1.48 (0.68), residues: 63 loop : 0.33 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 224 TYR 0.009 0.001 TYR A 465 PHE 0.014 0.001 PHE B 156 TRP 0.012 0.001 TRP B 263 HIS 0.002 0.000 HIS B 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9058) covalent geometry : angle 0.54630 / 0.26 (12291) hydrogen bonds : bond 0.04494 / 3.02 ( 562) hydrogen bonds : angle 3.64172 / 2.62 ( 1623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 285 MET cc_start: 0.8363 (tmm) cc_final: 0.8105 (tmm) REVERT: B 310 TYR cc_start: 0.7978 (t80) cc_final: 0.7234 (t80) REVERT: B 624 ASP cc_start: 0.8953 (t0) cc_final: 0.8566 (p0) REVERT: B 645 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8588 (mm) REVERT: D 124 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6312 (mtp) REVERT: A 301 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8510 (mm-30) outliers start: 21 outliers final: 11 residues processed: 131 average time/residue: 0.0716 time to fit residues: 14.0895 Evaluate side-chains 122 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 333 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089970 restraints weight = 17559.377| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.13 r_work: 0.3082 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9058 Z= 0.122 Angle : 0.566 14.953 12291 Z= 0.267 Chirality : 0.039 0.176 1423 Planarity : 0.003 0.035 1569 Dihedral : 5.834 78.068 1275 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.65 % Allowed : 12.62 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.26), residues: 1124 helix: 2.19 (0.20), residues: 711 sheet: 1.41 (0.68), residues: 63 loop : 0.37 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.009 0.001 TYR A 465 PHE 0.011 0.001 PHE A 390 TRP 0.012 0.001 TRP B 263 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9058) covalent geometry : angle 0.56649 / 0.27 (12291) hydrogen bonds : bond 0.04492 / 3.00 ( 562) hydrogen bonds : angle 3.64716 / 2.62 ( 1623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: B 138 MET cc_start: 0.8707 (tpp) cc_final: 0.8204 (tpp) REVERT: B 285 MET cc_start: 0.8319 (tmm) cc_final: 0.8044 (tmm) REVERT: B 310 TYR cc_start: 0.7945 (t80) cc_final: 0.7487 (t80) REVERT: B 624 ASP cc_start: 0.8974 (t0) cc_final: 0.8607 (p0) REVERT: B 645 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8575 (mm) REVERT: D 124 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6350 (mtp) outliers start: 16 outliers final: 10 residues processed: 121 average time/residue: 0.0794 time to fit residues: 14.4132 Evaluate side-chains 120 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TRP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 333 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 3.9990 chunk 87 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.7383 > 50:) chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 562 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087049 restraints weight = 17801.228| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.09 r_work: 0.3031 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9058 Z= 0.197 Angle : 0.616 12.764 12291 Z= 0.296 Chirality : 0.041 0.187 1423 Planarity : 0.004 0.037 1569 Dihedral : 6.151 88.411 1275 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.65 % Allowed : 13.65 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.26), residues: 1124 helix: 1.99 (0.19), residues: 711 sheet: 1.38 (0.68), residues: 63 loop : 0.28 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.012 0.001 TYR A 555 PHE 0.017 0.002 PHE A 390 TRP 0.011 0.001 TRP B 263 HIS 0.003 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 9058) covalent geometry : angle 0.61575 / 0.30 (12291) hydrogen bonds : bond 0.05175 / 3.44 ( 562) hydrogen bonds : angle 3.86392 / 2.78 ( 1623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 285 MET cc_start: 0.8386 (tmm) cc_final: 0.8092 (tmm) REVERT: B 299 HIS cc_start: 0.8767 (t-170) cc_final: 0.8408 (t-170) REVERT: B 310 TYR cc_start: 0.7942 (t80) cc_final: 0.7379 (t80) REVERT: B 624 ASP cc_start: 0.8962 (t0) cc_final: 0.8614 (p0) REVERT: B 645 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8588 (mm) REVERT: A 301 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8438 (mm-30) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.0812 time to fit residues: 13.7879 Evaluate side-chains 114 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain D residue 134 TRP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 562 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089288 restraints weight = 17704.094| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.13 r_work: 0.3071 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9058 Z= 0.118 Angle : 0.571 13.046 12291 Z= 0.270 Chirality : 0.039 0.213 1423 Planarity : 0.003 0.039 1569 Dihedral : 5.922 83.992 1275 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 13.96 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.26), residues: 1124 helix: 2.19 (0.20), residues: 710 sheet: 1.25 (0.67), residues: 63 loop : 0.31 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.009 0.001 TYR A 465 PHE 0.018 0.001 PHE B 156 TRP 0.008 0.001 TRP B 263 HIS 0.002 0.000 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9058) covalent geometry : angle 0.57083 / 0.27 (12291) hydrogen bonds : bond 0.04573 / 3.06 ( 562) hydrogen bonds : angle 3.67002 / 2.64 ( 1623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: B 138 MET cc_start: 0.8904 (tpp) cc_final: 0.8346 (tpp) REVERT: B 285 MET cc_start: 0.8401 (tmm) cc_final: 0.8111 (tmm) REVERT: B 299 HIS cc_start: 0.8666 (t-170) cc_final: 0.8289 (t-170) REVERT: B 310 TYR cc_start: 0.7901 (t80) cc_final: 0.7477 (t80) REVERT: B 645 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 301 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8399 (mm-30) outliers start: 16 outliers final: 11 residues processed: 116 average time/residue: 0.0729 time to fit residues: 12.8158 Evaluate side-chains 117 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 9 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.091064 restraints weight = 17514.493| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.11 r_work: 0.3100 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9058 Z= 0.109 Angle : 0.569 11.897 12291 Z= 0.269 Chirality : 0.039 0.229 1423 Planarity : 0.003 0.037 1569 Dihedral : 5.714 78.552 1275 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.14 % Allowed : 14.79 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.26), residues: 1124 helix: 2.28 (0.20), residues: 710 sheet: 1.28 (0.67), residues: 63 loop : 0.33 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.009 0.001 TYR A 465 PHE 0.018 0.001 PHE B 156 TRP 0.013 0.001 TRP B 263 HIS 0.003 0.000 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 9058) covalent geometry : angle 0.56917 / 0.27 (12291) hydrogen bonds : bond 0.04271 / 2.86 ( 562) hydrogen bonds : angle 3.59017 / 2.58 ( 1623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: B 138 MET cc_start: 0.8886 (tpp) cc_final: 0.8248 (tpp) REVERT: B 285 MET cc_start: 0.8382 (tmm) cc_final: 0.8101 (tmm) REVERT: B 299 HIS cc_start: 0.8542 (t-170) cc_final: 0.8192 (t-170) REVERT: B 310 TYR cc_start: 0.7867 (t80) cc_final: 0.7413 (t80) REVERT: B 417 GLU cc_start: 0.8332 (tp30) cc_final: 0.7978 (tp30) REVERT: B 645 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8573 (mm) REVERT: D 124 MET cc_start: 0.6808 (mtp) cc_final: 0.6499 (mtm) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.0742 time to fit residues: 13.4166 Evaluate side-chains 117 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain D residue 134 TRP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 0.0670 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 0.0970 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091923 restraints weight = 17470.780| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.10 r_work: 0.3116 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9058 Z= 0.106 Angle : 0.563 11.346 12291 Z= 0.264 Chirality : 0.038 0.192 1423 Planarity : 0.003 0.036 1569 Dihedral : 5.566 75.432 1275 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.03 % Allowed : 14.89 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.26), residues: 1124 helix: 2.37 (0.20), residues: 710 sheet: 1.29 (0.68), residues: 63 loop : 0.39 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.018 0.001 TYR A 428 PHE 0.009 0.001 PHE A 275 TRP 0.011 0.001 TRP B 263 HIS 0.003 0.000 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 9058) covalent geometry : angle 0.56289 / 0.26 (12291) hydrogen bonds : bond 0.03991 / 2.67 ( 562) hydrogen bonds : angle 3.49820 / 2.51 ( 1623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: B 138 MET cc_start: 0.8886 (tpp) cc_final: 0.8272 (tpp) REVERT: B 285 MET cc_start: 0.8306 (tmm) cc_final: 0.8011 (tmm) REVERT: B 299 HIS cc_start: 0.8381 (t-170) cc_final: 0.8053 (t-170) REVERT: B 310 TYR cc_start: 0.7873 (t80) cc_final: 0.7424 (t80) REVERT: B 417 GLU cc_start: 0.8306 (tp30) cc_final: 0.7952 (tp30) REVERT: B 624 ASP cc_start: 0.8999 (t0) cc_final: 0.8315 (p0) REVERT: B 645 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8572 (mm) outliers start: 10 outliers final: 7 residues processed: 118 average time/residue: 0.0795 time to fit residues: 13.9056 Evaluate side-chains 113 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain D residue 134 TRP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 0.0570 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.111005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091100 restraints weight = 17356.304| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.08 r_work: 0.3102 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9058 Z= 0.115 Angle : 0.582 12.861 12291 Z= 0.271 Chirality : 0.038 0.167 1423 Planarity : 0.003 0.037 1569 Dihedral : 5.609 78.403 1275 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.03 % Allowed : 15.10 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.26), residues: 1124 helix: 2.35 (0.20), residues: 712 sheet: 1.31 (0.68), residues: 63 loop : 0.34 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.011 0.001 TYR A 309 PHE 0.025 0.002 PHE A 447 TRP 0.011 0.001 TRP B 263 HIS 0.002 0.000 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9058) covalent geometry : angle 0.58199 / 0.27 (12291) hydrogen bonds : bond 0.04142 / 2.76 ( 562) hydrogen bonds : angle 3.54344 / 2.54 ( 1623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.73 seconds wall clock time: 25 minutes 43.87 seconds (1543.87 seconds total)