Starting phenix.real_space_refine on Wed Feb 4 06:54:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ocj_70317/02_2026/9ocj_70317.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ocj_70317/02_2026/9ocj_70317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ocj_70317/02_2026/9ocj_70317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ocj_70317/02_2026/9ocj_70317.map" model { file = "/net/cci-nas-00/data/ceres_data/9ocj_70317/02_2026/9ocj_70317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ocj_70317/02_2026/9ocj_70317.cif" } resolution = 3.0 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= 0.017 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 6 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 5724 2.51 5 N 1559 2.21 5 O 1673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9006 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4305 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 20, 'TRANS': 529} Chain: "D" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 273 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4364 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 23, 'TRANS': 540} Chain breaks: 1 Chain: "B" 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} 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: 2.29, per 1000 atoms: 0.25 Number of scatterers: 9006 At special positions: 0 Unit cell: (71.38, 88.58, 137.6, 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 42 16.00 P 6 15.00 Mg 2 11.99 O 1673 8.00 N 1559 7.00 C 5724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 328.6 milliseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 72.5% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.668A pdb=" N LEU B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 removed outlier: 4.033A pdb=" N ALA B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.644A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 234 Processing helix chain 'B' and resid 235 through 236 No H-bonds generated for 'chain 'B' and resid 235 through 236' Processing helix chain 'B' and resid 237 through 238 No H-bonds generated for 'chain 'B' and resid 237 through 238' Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.584A pdb=" N THR B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 256 through 262 removed outlier: 3.929A pdb=" N MET B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 289 removed outlier: 3.567A pdb=" N LEU B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE B 288 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 303 through 338 removed outlier: 3.540A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.800A 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 401 removed outlier: 4.001A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 440 removed outlier: 3.809A pdb=" N GLN B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 437 " --> pdb=" O MET B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 449 removed outlier: 4.062A 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: 3.581A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 545 " --> pdb=" O TYR B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 590 Processing helix chain 'B' and resid 594 through 598 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 644 removed outlier: 3.632A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.508A pdb=" N ARG B 668 " --> pdb=" O THR B 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 63 removed outlier: 3.581A pdb=" N ARG D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ARG D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR D 62 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 179 through 182 removed outlier: 4.256A pdb=" N SER A 182 " --> pdb=" O CYS A 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.769A pdb=" N PHE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 270 removed outlier: 3.627A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 290 through 324 removed outlier: 3.765A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 319 " --> pdb=" O CYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.930A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 3.661A pdb=" N VAL A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 373 removed outlier: 3.922A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 436 removed outlier: 3.670A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 475 removed outlier: 3.639A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 456 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 3.795A 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 475 through 484 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 removed outlier: 3.635A pdb=" N HIS A 578 " --> pdb=" O HIS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 644 through 658 Processing helix chain 'A' and resid 674 through 687 removed outlier: 3.718A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 694 removed outlier: 4.171A pdb=" N TYR A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.894A pdb=" N GLU A 707 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN A 708 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 734 through 742 Processing sheet with id=AA1, first strand: chain 'B' and resid 486 through 493 removed outlier: 6.884A pdb=" N LYS B 487 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER B 474 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.429A pdb=" N THR B 499 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 528 removed outlier: 6.747A pdb=" N GLN A 522 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER A 509 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU A 524 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 526 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.706A pdb=" N VAL A 533 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 713 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA A 535 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU A 715 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 537 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 722 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU A 716 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1686 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: 1.51 Time building geometry restraints manager: 1.32 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: 2966 1.34 - 1.46: 1949 1.46 - 1.58: 4189 1.58 - 1.70: 7 1.70 - 1.81: 69 Bond restraints: 9180 Sorted by residual: bond pdb=" CA PHE D 42 " pdb=" C PHE D 42 " ideal model delta sigma weight residual 1.523 1.606 -0.083 1.35e-02 5.49e+03 3.76e+01 bond pdb=" N TYR D 50 " pdb=" CA TYR D 50 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.28e-02 6.10e+03 3.79e+00 bond pdb=" N LYS D 51 " pdb=" CA LYS D 51 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.19e-02 7.06e+03 3.64e+00 bond pdb=" CB MET A 202 " pdb=" CG MET A 202 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CA PHE A 624 " pdb=" C PHE A 624 " ideal model delta sigma weight residual 1.521 1.534 -0.014 1.27e-02 6.20e+03 1.18e+00 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 12352 2.66 - 5.32: 87 5.32 - 7.98: 14 7.98 - 10.63: 3 10.63 - 13.29: 2 Bond angle restraints: 12458 Sorted by residual: angle pdb=" N LYS D 43 " pdb=" CA LYS D 43 " pdb=" C LYS D 43 " ideal model delta sigma weight residual 110.35 123.64 -13.29 1.36e+00 5.41e-01 9.55e+01 angle pdb=" CA PHE D 42 " pdb=" C PHE D 42 " pdb=" N LYS D 43 " ideal model delta sigma weight residual 117.22 110.07 7.15 1.17e+00 7.31e-01 3.73e+01 angle pdb=" CA PHE D 42 " pdb=" C PHE D 42 " pdb=" O PHE D 42 " ideal model delta sigma weight residual 120.63 127.13 -6.50 1.08e+00 8.57e-01 3.63e+01 angle pdb=" N PHE D 42 " pdb=" CA PHE D 42 " pdb=" C PHE D 42 " ideal model delta sigma weight residual 111.33 118.22 -6.89 1.21e+00 6.83e-01 3.24e+01 angle pdb=" N TRP D 49 " pdb=" CA TRP D 49 " pdb=" C TRP D 49 " ideal model delta sigma weight residual 111.28 117.31 -6.03 1.09e+00 8.42e-01 3.06e+01 ... (remaining 12453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 5012 17.69 - 35.38: 379 35.38 - 53.07: 98 53.07 - 70.76: 39 70.76 - 88.44: 11 Dihedral angle restraints: 5539 sinusoidal: 2249 harmonic: 3290 Sorted by residual: dihedral pdb=" CA ARG A 694 " pdb=" C ARG A 694 " pdb=" N SER A 695 " pdb=" CA SER A 695 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" N TYR D 50 " pdb=" C TYR D 50 " pdb=" CA TYR D 50 " pdb=" CB TYR D 50 " ideal model delta harmonic sigma weight residual 122.80 114.00 8.80 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C PHE D 42 " pdb=" N PHE D 42 " pdb=" CA PHE D 42 " pdb=" CB PHE D 42 " ideal model delta harmonic sigma weight residual -122.60 -131.25 8.65 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 5536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1350 0.079 - 0.159: 74 0.159 - 0.238: 2 0.238 - 0.317: 3 0.317 - 0.397: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA LYS D 43 " pdb=" N LYS D 43 " pdb=" C LYS D 43 " pdb=" CB LYS D 43 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TRP D 49 " pdb=" N TRP D 49 " pdb=" C TRP D 49 " pdb=" CB TRP D 49 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA PHE D 42 " pdb=" N PHE D 42 " pdb=" C PHE D 42 " pdb=" CB PHE D 42 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1427 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 300 " 0.064 5.00e-02 4.00e+02 9.86e-02 1.55e+01 pdb=" N PRO B 301 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 50 " 0.026 2.00e-02 2.50e+03 1.70e-02 5.80e+00 pdb=" CG TYR D 50 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 50 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 50 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 42 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C PHE D 42 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE D 42 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS D 43 " -0.010 2.00e-02 2.50e+03 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 41 2.59 - 3.17: 7647 3.17 - 3.75: 13551 3.75 - 4.32: 18117 4.32 - 4.90: 30915 Nonbonded interactions: 70271 Sorted by model distance: nonbonded pdb=" OG SER A 545 " pdb="MG MG A1002 " model vdw 2.014 2.170 nonbonded pdb=" O2B ATP B 701 " pdb="MG MG B 702 " model vdw 2.074 2.170 nonbonded pdb=" O1G ATP A1001 " pdb="MG MG A1002 " model vdw 2.133 2.170 nonbonded pdb=" OE1 GLN B 551 " pdb="MG MG B 702 " model vdw 2.134 2.170 nonbonded pdb=" O3G ATP B 701 " pdb="MG MG B 702 " model vdw 2.140 2.170 ... (remaining 70266 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: 8.620 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 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 0.083 9180 Z= 0.167 Angle : 0.626 13.293 12458 Z= 0.360 Chirality : 0.042 0.397 1430 Planarity : 0.004 0.099 1587 Dihedral : 14.916 88.444 3427 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % 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 (0.25), residues: 1135 helix: 2.15 (0.19), residues: 710 sheet: 1.99 (0.60), residues: 79 loop : 0.20 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 668 TYR 0.039 0.001 TYR D 50 PHE 0.016 0.002 PHE D 58 TRP 0.012 0.001 TRP A 308 HIS 0.006 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9180) covalent geometry : angle 0.62592 (12458) hydrogen bonds : bond 0.15502 ( 583) hydrogen bonds : angle 5.02512 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.294 Fit side-chains REVERT: D 67 SER cc_start: 0.9037 (t) cc_final: 0.8773 (p) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4491 time to fit residues: 49.1949 Evaluate side-chains 85 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.092294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.069060 restraints weight = 18109.266| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.75 r_work: 0.2830 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9180 Z= 0.147 Angle : 0.555 9.718 12458 Z= 0.277 Chirality : 0.040 0.292 1430 Planarity : 0.004 0.077 1587 Dihedral : 8.770 81.855 1312 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.13 % Allowed : 9.22 % Favored : 89.65 % 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: 2.53 (0.26), residues: 1135 helix: 2.28 (0.19), residues: 729 sheet: 1.97 (0.63), residues: 79 loop : 0.25 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 651 TYR 0.011 0.001 TYR B 376 PHE 0.019 0.002 PHE A 276 TRP 0.010 0.001 TRP B 263 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9180) covalent geometry : angle 0.55550 (12458) hydrogen bonds : bond 0.06530 ( 583) hydrogen bonds : angle 4.19278 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: D 67 SER cc_start: 0.8928 (t) cc_final: 0.8583 (p) REVERT: A 199 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7185 (mp) REVERT: A 335 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9201 (mp) outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 0.4181 time to fit residues: 43.1331 Evaluate side-chains 92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 681 GLN A 642 GLN A 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066678 restraints weight = 18411.382| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.75 r_work: 0.2787 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9180 Z= 0.209 Angle : 0.578 9.732 12458 Z= 0.291 Chirality : 0.042 0.302 1430 Planarity : 0.004 0.067 1587 Dihedral : 8.141 81.464 1312 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.25 % Allowed : 9.43 % Favored : 88.32 % 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: 2.42 (0.25), residues: 1135 helix: 2.27 (0.19), residues: 727 sheet: 1.69 (0.62), residues: 81 loop : 0.10 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.011 0.001 TYR B 376 PHE 0.015 0.002 PHE B 302 TRP 0.011 0.001 TRP A 308 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 9180) covalent geometry : angle 0.57835 (12458) hydrogen bonds : bond 0.06928 ( 583) hydrogen bonds : angle 4.20483 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.325 Fit side-chains REVERT: B 668 ARG cc_start: 0.8401 (mmp80) cc_final: 0.7367 (mmm-85) REVERT: D 67 SER cc_start: 0.8889 (t) cc_final: 0.8482 (p) REVERT: A 199 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7224 (mp) REVERT: A 210 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7202 (mmm-85) REVERT: A 335 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9155 (mp) REVERT: A 433 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8517 (mm) REVERT: A 507 ASP cc_start: 0.8766 (t0) cc_final: 0.8472 (t0) REVERT: A 659 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8470 (mtt-85) outliers start: 22 outliers final: 12 residues processed: 102 average time/residue: 0.4581 time to fit residues: 50.6415 Evaluate side-chains 101 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 659 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 87 optimal weight: 0.0070 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 ASN A 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.069678 restraints weight = 18319.829| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.79 r_work: 0.2846 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9180 Z= 0.125 Angle : 0.520 9.281 12458 Z= 0.255 Chirality : 0.039 0.298 1430 Planarity : 0.003 0.058 1587 Dihedral : 7.590 83.234 1312 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.64 % Allowed : 10.35 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.26), residues: 1135 helix: 2.56 (0.19), residues: 728 sheet: 1.67 (0.63), residues: 80 loop : 0.09 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 651 TYR 0.010 0.001 TYR B 376 PHE 0.013 0.001 PHE A 479 TRP 0.009 0.001 TRP A 308 HIS 0.002 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9180) covalent geometry : angle 0.51991 (12458) hydrogen bonds : bond 0.05801 ( 583) hydrogen bonds : angle 3.85952 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 387 VAL cc_start: 0.8538 (t) cc_final: 0.8300 (p) REVERT: B 668 ARG cc_start: 0.8420 (mmp80) cc_final: 0.7440 (mmm-85) REVERT: D 67 SER cc_start: 0.8871 (t) cc_final: 0.8454 (p) REVERT: A 199 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7256 (mp) REVERT: A 433 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 507 ASP cc_start: 0.8695 (t0) cc_final: 0.8413 (t0) outliers start: 16 outliers final: 6 residues processed: 98 average time/residue: 0.3902 time to fit residues: 41.8439 Evaluate side-chains 94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 0.0070 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069440 restraints weight = 18243.547| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.79 r_work: 0.2831 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9180 Z= 0.136 Angle : 0.528 9.745 12458 Z= 0.258 Chirality : 0.039 0.289 1430 Planarity : 0.003 0.060 1587 Dihedral : 7.384 79.072 1312 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.84 % Allowed : 10.35 % Favored : 87.81 % 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: 2.84 (0.26), residues: 1135 helix: 2.66 (0.19), residues: 728 sheet: 1.63 (0.63), residues: 80 loop : 0.15 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 651 TYR 0.010 0.001 TYR B 376 PHE 0.012 0.001 PHE B 588 TRP 0.011 0.001 TRP B 263 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9180) covalent geometry : angle 0.52777 (12458) hydrogen bonds : bond 0.05791 ( 583) hydrogen bonds : angle 3.81174 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 387 VAL cc_start: 0.8503 (t) cc_final: 0.8266 (p) REVERT: B 668 ARG cc_start: 0.8453 (mmp80) cc_final: 0.7493 (mmm-85) REVERT: D 67 SER cc_start: 0.8886 (t) cc_final: 0.8457 (p) REVERT: A 199 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7243 (mp) REVERT: A 335 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9137 (mp) REVERT: A 433 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8394 (mm) REVERT: A 507 ASP cc_start: 0.8695 (t0) cc_final: 0.8404 (t0) REVERT: A 659 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8394 (mtt-85) outliers start: 18 outliers final: 7 residues processed: 101 average time/residue: 0.4621 time to fit residues: 50.8630 Evaluate side-chains 96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 659 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.0570 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.070017 restraints weight = 18224.941| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.77 r_work: 0.2853 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9180 Z= 0.124 Angle : 0.531 10.604 12458 Z= 0.254 Chirality : 0.039 0.345 1430 Planarity : 0.003 0.057 1587 Dihedral : 7.226 75.528 1312 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.43 % Allowed : 10.96 % Favored : 87.60 % 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: 2.97 (0.26), residues: 1135 helix: 2.78 (0.19), residues: 727 sheet: 1.59 (0.63), residues: 80 loop : 0.18 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 651 TYR 0.010 0.001 TYR B 376 PHE 0.012 0.001 PHE A 479 TRP 0.008 0.001 TRP B 263 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9180) covalent geometry : angle 0.53104 (12458) hydrogen bonds : bond 0.05438 ( 583) hydrogen bonds : angle 3.69467 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.366 Fit side-chains REVERT: B 387 VAL cc_start: 0.8477 (t) cc_final: 0.8247 (p) REVERT: D 67 SER cc_start: 0.8821 (t) cc_final: 0.8386 (p) REVERT: A 199 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 210 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7992 (mmm160) REVERT: A 335 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9131 (mp) REVERT: A 507 ASP cc_start: 0.8668 (t0) cc_final: 0.8372 (t0) outliers start: 14 outliers final: 6 residues processed: 105 average time/residue: 0.4363 time to fit residues: 49.8834 Evaluate side-chains 92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.069457 restraints weight = 18324.448| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.77 r_work: 0.2836 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9180 Z= 0.137 Angle : 0.543 10.912 12458 Z= 0.261 Chirality : 0.040 0.350 1430 Planarity : 0.003 0.057 1587 Dihedral : 7.232 76.306 1312 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.97 % Rotamer: Outliers : 1.64 % Allowed : 11.37 % Favored : 86.99 % 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: 2.96 (0.26), residues: 1135 helix: 2.78 (0.19), residues: 727 sheet: 1.55 (0.62), residues: 80 loop : 0.18 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 659 TYR 0.010 0.001 TYR B 376 PHE 0.012 0.001 PHE B 588 TRP 0.007 0.001 TRP A 308 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9180) covalent geometry : angle 0.54294 (12458) hydrogen bonds : bond 0.05547 ( 583) hydrogen bonds : angle 3.72101 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: B 387 VAL cc_start: 0.8487 (t) cc_final: 0.8257 (p) REVERT: D 67 SER cc_start: 0.8837 (t) cc_final: 0.8398 (p) REVERT: A 199 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7271 (mp) REVERT: A 210 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.8076 (mmm160) REVERT: A 329 MET cc_start: 0.8219 (ttp) cc_final: 0.7835 (tmm) REVERT: A 335 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9165 (mp) REVERT: A 507 ASP cc_start: 0.8640 (t0) cc_final: 0.8362 (t0) outliers start: 16 outliers final: 9 residues processed: 100 average time/residue: 0.3920 time to fit residues: 42.7900 Evaluate side-chains 95 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.0670 chunk 84 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.071984 restraints weight = 18102.990| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.83 r_work: 0.2876 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9180 Z= 0.113 Angle : 0.540 11.736 12458 Z= 0.256 Chirality : 0.038 0.342 1430 Planarity : 0.003 0.052 1587 Dihedral : 6.904 73.132 1312 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.50 % Favored : 98.41 % Rotamer: Outliers : 1.02 % Allowed : 11.89 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.26), residues: 1135 helix: 2.88 (0.19), residues: 728 sheet: 1.54 (0.62), residues: 80 loop : 0.19 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.010 0.001 TYR B 376 PHE 0.024 0.001 PHE B 194 TRP 0.007 0.001 TRP A 308 HIS 0.002 0.000 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9180) covalent geometry : angle 0.54003 (12458) hydrogen bonds : bond 0.04916 ( 583) hydrogen bonds : angle 3.54484 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: B 387 VAL cc_start: 0.8438 (t) cc_final: 0.8220 (p) REVERT: B 414 ILE cc_start: 0.9051 (mm) cc_final: 0.8843 (pp) REVERT: A 199 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7246 (mp) REVERT: A 329 MET cc_start: 0.8326 (ttp) cc_final: 0.7904 (tmm) REVERT: A 358 GLU cc_start: 0.8591 (tt0) cc_final: 0.8324 (mt-10) REVERT: A 433 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (mm) REVERT: A 507 ASP cc_start: 0.8597 (t0) cc_final: 0.8302 (t0) outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 0.3992 time to fit residues: 43.2582 Evaluate side-chains 91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.070540 restraints weight = 18159.426| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.77 r_work: 0.2857 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9180 Z= 0.126 Angle : 0.549 11.869 12458 Z= 0.260 Chirality : 0.039 0.357 1430 Planarity : 0.003 0.055 1587 Dihedral : 6.886 74.266 1312 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.85 % Favored : 98.06 % Rotamer: Outliers : 1.13 % Allowed : 12.50 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.26), residues: 1135 helix: 2.86 (0.19), residues: 729 sheet: 1.53 (0.62), residues: 80 loop : 0.23 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.010 0.001 TYR B 376 PHE 0.014 0.001 PHE A 206 TRP 0.011 0.001 TRP B 263 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9180) covalent geometry : angle 0.54906 (12458) hydrogen bonds : bond 0.05128 ( 583) hydrogen bonds : angle 3.60686 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: B 387 VAL cc_start: 0.8473 (t) cc_final: 0.8247 (p) REVERT: B 414 ILE cc_start: 0.9061 (mm) cc_final: 0.8843 (pp) REVERT: A 199 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7275 (mp) REVERT: A 301 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: A 329 MET cc_start: 0.8332 (ttp) cc_final: 0.7877 (tmm) REVERT: A 507 ASP cc_start: 0.8595 (t0) cc_final: 0.8312 (t0) REVERT: A 659 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7643 (mtt-85) outliers start: 11 outliers final: 5 residues processed: 91 average time/residue: 0.4591 time to fit residues: 45.5143 Evaluate side-chains 91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 659 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.069009 restraints weight = 18247.824| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.77 r_work: 0.2833 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9180 Z= 0.149 Angle : 0.573 13.212 12458 Z= 0.273 Chirality : 0.040 0.364 1430 Planarity : 0.004 0.058 1587 Dihedral : 7.063 77.151 1312 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.03 % Favored : 97.89 % Rotamer: Outliers : 1.23 % Allowed : 12.70 % Favored : 86.07 % 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: 2.95 (0.26), residues: 1135 helix: 2.75 (0.19), residues: 730 sheet: 1.54 (0.63), residues: 80 loop : 0.21 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.010 0.001 TYR B 376 PHE 0.013 0.001 PHE B 588 TRP 0.017 0.001 TRP B 263 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9180) covalent geometry : angle 0.57252 (12458) hydrogen bonds : bond 0.05561 ( 583) hydrogen bonds : angle 3.74476 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 228 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: B 387 VAL cc_start: 0.8501 (t) cc_final: 0.8269 (p) REVERT: A 199 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7272 (mp) REVERT: A 301 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8462 (mt-10) REVERT: A 329 MET cc_start: 0.8353 (ttp) cc_final: 0.7901 (tmm) REVERT: A 507 ASP cc_start: 0.8599 (t0) cc_final: 0.8297 (t0) REVERT: A 659 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.7595 (mtt-85) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.4019 time to fit residues: 41.4153 Evaluate side-chains 93 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 659 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 chunk 56 optimal weight: 0.0050 chunk 83 optimal weight: 0.7980 overall best weight: 0.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.093658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.070281 restraints weight = 18087.734| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.77 r_work: 0.2856 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9180 Z= 0.125 Angle : 0.561 13.671 12458 Z= 0.265 Chirality : 0.040 0.360 1430 Planarity : 0.004 0.069 1587 Dihedral : 6.905 75.887 1312 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.50 % Favored : 98.41 % Rotamer: Outliers : 0.82 % Allowed : 13.22 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.26), residues: 1135 helix: 2.82 (0.19), residues: 730 sheet: 1.53 (0.62), residues: 80 loop : 0.25 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 210 TYR 0.010 0.001 TYR B 376 PHE 0.026 0.001 PHE B 302 TRP 0.018 0.001 TRP B 263 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9180) covalent geometry : angle 0.56088 (12458) hydrogen bonds : bond 0.05199 ( 583) hydrogen bonds : angle 3.65013 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2240.21 seconds wall clock time: 39 minutes 2.82 seconds (2342.82 seconds total)