Starting phenix.real_space_refine on Wed Sep 17 17:03:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mq6_48514/09_2025/9mq6_48514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mq6_48514/09_2025/9mq6_48514.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 { model { file = "/net/cci-nas-00/data/ceres_data/9mq6_48514/09_2025/9mq6_48514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mq6_48514/09_2025/9mq6_48514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mq6_48514/09_2025/9mq6_48514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mq6_48514/09_2025/9mq6_48514.map" } 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= 0.001 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 47 5.16 5 C 6201 2.51 5 N 1749 2.21 5 O 1910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9917 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4475 Classifications: {'peptide': 573} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 1 Chain: "B" Number of atoms: 4423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4423 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 537} Chain breaks: 1 Chain: "C" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 903 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.35, per 1000 atoms: 0.24 Number of scatterers: 9917 At special positions: 0 Unit cell: (97.405, 110.11, 127.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 10 15.00 O 1910 8.00 N 1749 7.00 C 6201 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: 0.90 Conformation dependent library (CDL) restraints added in 372.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 55.7% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.211A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.675A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.509A pdb=" N ILE A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.537A pdb=" N GLU A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.922A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.802A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 4.186A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.876A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.635A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.633A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.586A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.964A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.730A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.527A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 715 removed outlier: 4.037A pdb=" N THR A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.981A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 765 removed outlier: 4.307A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.565A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.524A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.008A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.169A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.689A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.964A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.061A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.855A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.802A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 430 Processing helix chain 'B' and resid 438 through 444 removed outlier: 3.632A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.519A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.766A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.614A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.785A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.537A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.708A pdb=" N ASP B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.518A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 removed outlier: 3.548A pdb=" N ARG B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 680 removed outlier: 3.615A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 710 Processing helix chain 'B' and resid 711 through 715 removed outlier: 3.980A pdb=" N GLN B 714 " --> pdb=" O ARG B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 4.052A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 766 Processing helix chain 'C' and resid 621 through 634 removed outlier: 3.623A pdb=" N MET C 627 " --> pdb=" O TYR C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 655 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 removed outlier: 7.581A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 269 removed outlier: 6.584A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.422A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 578 through 580 Processing sheet with id=AA6, first strand: chain 'C' and resid 592 through 596 445 hydrogen bonds defined for protein. 1272 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: 1.42 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3388 1.34 - 1.46: 1413 1.46 - 1.57: 5201 1.57 - 1.69: 12 1.69 - 1.81: 82 Bond restraints: 10096 Sorted by residual: bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C ALA B 259 " pdb=" N ASN B 260 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.84e-01 bond pdb=" C ALA B 297 " pdb=" N PRO B 298 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.73e-01 bond pdb=" CG PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.33e-01 ... (remaining 10091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 13485 1.62 - 3.25: 127 3.25 - 4.87: 31 4.87 - 6.49: 9 6.49 - 8.12: 1 Bond angle restraints: 13653 Sorted by residual: angle pdb=" CA LEU A 306 " pdb=" CB LEU A 306 " pdb=" CG LEU A 306 " ideal model delta sigma weight residual 116.30 124.42 -8.12 3.50e+00 8.16e-02 5.38e+00 angle pdb=" C VAL B 258 " pdb=" N ALA B 259 " pdb=" CA ALA B 259 " ideal model delta sigma weight residual 122.31 118.57 3.74 1.81e+00 3.05e-01 4.28e+00 angle pdb=" C ALA B 259 " pdb=" N ASN B 260 " pdb=" CA ASN B 260 " ideal model delta sigma weight residual 121.54 125.21 -3.67 1.91e+00 2.74e-01 3.70e+00 angle pdb=" C PHE B 290 " pdb=" N GLU B 291 " pdb=" CA GLU B 291 " ideal model delta sigma weight residual 122.09 118.68 3.41 1.79e+00 3.12e-01 3.63e+00 angle pdb=" O1B ADP B 901 " pdb=" PB ADP B 901 " pdb=" O3B ADP B 901 " ideal model delta sigma weight residual 119.90 114.26 5.64 3.00e+00 1.11e-01 3.53e+00 ... (remaining 13648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.98: 5984 20.98 - 41.96: 218 41.96 - 62.93: 21 62.93 - 83.91: 3 83.91 - 104.89: 3 Dihedral angle restraints: 6229 sinusoidal: 2640 harmonic: 3589 Sorted by residual: dihedral pdb=" O1A ANP A 902 " pdb=" O3A ANP A 902 " pdb=" PA ANP A 902 " pdb=" PB ANP A 902 " ideal model delta sinusoidal sigma weight residual 83.11 -21.78 104.89 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA ALA B 259 " pdb=" C ALA B 259 " pdb=" N ASN B 260 " pdb=" CA ASN B 260 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" O1B ANP B 902 " pdb=" N3B ANP B 902 " pdb=" PB ANP B 902 " pdb=" PG ANP B 902 " ideal model delta sinusoidal sigma weight residual 35.15 -61.12 96.27 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 6226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 849 0.026 - 0.052: 399 0.052 - 0.078: 139 0.078 - 0.103: 68 0.103 - 0.129: 52 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 645 " pdb=" N ILE B 645 " pdb=" C ILE B 645 " pdb=" CB ILE B 645 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1504 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 544 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO A 545 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 544 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 545 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 297 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 298 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " -0.020 5.00e-02 4.00e+02 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1768 2.77 - 3.30: 9608 3.30 - 3.83: 15081 3.83 - 4.37: 17318 4.37 - 4.90: 29908 Nonbonded interactions: 73683 Sorted by model distance: nonbonded pdb=" OH TYR B 244 " pdb=" OE1 GLU B 366 " model vdw 2.234 3.040 nonbonded pdb=" O ASN B 624 " pdb=" OH TYR B 755 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP B 649 " pdb=" OG SER B 652 " model vdw 2.267 3.040 nonbonded pdb=" O ARG A 313 " pdb=" OG1 THR A 316 " model vdw 2.272 3.040 nonbonded pdb=" O ALA A 439 " pdb=" ND2 ASN A 443 " model vdw 2.274 3.120 ... (remaining 73678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 193 through 769 or resid 901 through 902)) selection = chain 'B' } 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: 3.240 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 0.023 10096 Z= 0.119 Angle : 0.475 8.118 13653 Z= 0.230 Chirality : 0.041 0.129 1507 Planarity : 0.004 0.044 1793 Dihedral : 10.599 104.889 3905 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.48 % Allowed : 6.58 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1242 helix: 1.44 (0.23), residues: 570 sheet: 0.63 (0.45), residues: 150 loop : -0.45 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 653 TYR 0.007 0.001 TYR B 644 PHE 0.007 0.001 PHE B 758 TRP 0.006 0.001 TRP B 454 HIS 0.002 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00269 (10096) covalent geometry : angle 0.47492 (13653) hydrogen bonds : bond 0.18675 ( 445) hydrogen bonds : angle 5.99050 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 226 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 368 ASP cc_start: 0.7847 (t70) cc_final: 0.7529 (t70) REVERT: A 398 GLN cc_start: 0.8827 (tp40) cc_final: 0.8627 (tp40) REVERT: A 442 MET cc_start: 0.8724 (tmm) cc_final: 0.8433 (tmm) REVERT: A 450 ASP cc_start: 0.8437 (t0) cc_final: 0.8125 (t0) REVERT: A 607 GLU cc_start: 0.8336 (tp30) cc_final: 0.7905 (tp30) REVERT: A 663 LYS cc_start: 0.5956 (tttt) cc_final: 0.5684 (tmtt) REVERT: B 565 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8458 (tttt) REVERT: B 599 ARG cc_start: 0.8616 (ptp-110) cc_final: 0.7372 (mmm160) REVERT: B 614 LYS cc_start: 0.3857 (tmtt) cc_final: 0.2786 (tttm) REVERT: B 766 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.6364 (tpt170) REVERT: C 561 ASP cc_start: 0.8434 (p0) cc_final: 0.8127 (p0) REVERT: C 562 ARG cc_start: 0.6609 (mmt180) cc_final: 0.6036 (mmt180) REVERT: C 646 LYS cc_start: 0.9174 (ttmm) cc_final: 0.8958 (tmtt) outliers start: 5 outliers final: 2 residues processed: 231 average time/residue: 0.1433 time to fit residues: 42.0322 Evaluate side-chains 170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 538 ASN A 750 ASN B 348 ASN B 398 GLN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084195 restraints weight = 19363.419| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.13 r_work: 0.3032 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10096 Z= 0.204 Angle : 0.620 8.996 13653 Z= 0.305 Chirality : 0.044 0.147 1507 Planarity : 0.005 0.048 1793 Dihedral : 8.129 107.636 1442 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.91 % Allowed : 9.91 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 0.91 (0.25), residues: 1242 helix: 1.62 (0.22), residues: 584 sheet: 0.39 (0.44), residues: 151 loop : -0.49 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 338 TYR 0.011 0.001 TYR C 612 PHE 0.010 0.001 PHE B 758 TRP 0.009 0.001 TRP C 580 HIS 0.009 0.001 HIS C 633 Details of bonding type rmsd covalent geometry : bond 0.00482 (10096) covalent geometry : angle 0.62042 (13653) hydrogen bonds : bond 0.05070 ( 445) hydrogen bonds : angle 4.35050 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8689 (tm-30) REVERT: A 368 ASP cc_start: 0.8499 (t70) cc_final: 0.8002 (t70) REVERT: A 442 MET cc_start: 0.8949 (tmm) cc_final: 0.8670 (tmm) REVERT: A 450 ASP cc_start: 0.8831 (t0) cc_final: 0.8526 (t0) REVERT: A 742 PHE cc_start: 0.8568 (m-80) cc_final: 0.8246 (m-10) REVERT: B 556 GLU cc_start: 0.8811 (mp0) cc_final: 0.8422 (mp0) REVERT: B 558 ASN cc_start: 0.8885 (t0) cc_final: 0.8402 (t0) REVERT: B 599 ARG cc_start: 0.8876 (ptp-110) cc_final: 0.7530 (mmm160) REVERT: B 614 LYS cc_start: 0.4321 (tmtt) cc_final: 0.2961 (tttm) REVERT: B 738 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8544 (tm-30) REVERT: B 766 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.6423 (tpt170) REVERT: C 557 TYR cc_start: 0.7172 (m-80) cc_final: 0.6841 (m-80) REVERT: C 562 ARG cc_start: 0.6449 (mmt180) cc_final: 0.6032 (mmt180) REVERT: C 605 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: C 638 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8996 (m-80) REVERT: C 646 LYS cc_start: 0.9265 (ttmm) cc_final: 0.8987 (tmtt) REVERT: C 654 GLN cc_start: 0.9171 (tt0) cc_final: 0.8921 (tm-30) outliers start: 20 outliers final: 15 residues processed: 184 average time/residue: 0.1147 time to fit residues: 28.3651 Evaluate side-chains 179 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.0070 chunk 27 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 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 = 0.3569 r_free = 0.3569 target = 0.106280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083342 restraints weight = 19224.970| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.29 r_work: 0.3023 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10096 Z= 0.138 Angle : 0.555 8.419 13653 Z= 0.268 Chirality : 0.042 0.137 1507 Planarity : 0.004 0.046 1793 Dihedral : 8.038 109.139 1442 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.38 % Allowed : 10.20 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.06 (0.25), residues: 1242 helix: 1.84 (0.22), residues: 589 sheet: 0.41 (0.44), residues: 150 loop : -0.55 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 465 TYR 0.007 0.001 TYR C 608 PHE 0.007 0.001 PHE B 758 TRP 0.006 0.001 TRP C 580 HIS 0.006 0.001 HIS C 633 Details of bonding type rmsd covalent geometry : bond 0.00323 (10096) covalent geometry : angle 0.55452 (13653) hydrogen bonds : bond 0.04133 ( 445) hydrogen bonds : angle 3.94227 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8506 (t70) cc_final: 0.8002 (t70) REVERT: A 442 MET cc_start: 0.9000 (tmm) cc_final: 0.8716 (tmm) REVERT: A 450 ASP cc_start: 0.8846 (t0) cc_final: 0.8540 (t0) REVERT: B 561 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: B 599 ARG cc_start: 0.8861 (ptp-110) cc_final: 0.7468 (mmm160) REVERT: B 606 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9149 (t) REVERT: B 614 LYS cc_start: 0.4379 (tmtt) cc_final: 0.3416 (tmtt) REVERT: B 738 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8595 (tm-30) REVERT: B 766 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.6445 (tpt170) REVERT: C 562 ARG cc_start: 0.6278 (mmt180) cc_final: 0.5846 (mmt180) REVERT: C 632 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8802 (ttpt) REVERT: C 633 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8752 (m90) REVERT: C 638 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8948 (m-80) REVERT: C 646 LYS cc_start: 0.9224 (ttmm) cc_final: 0.8927 (tmtt) REVERT: C 654 GLN cc_start: 0.9130 (tt0) cc_final: 0.8843 (tm-30) outliers start: 25 outliers final: 10 residues processed: 181 average time/residue: 0.1048 time to fit residues: 25.6956 Evaluate side-chains 174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.084381 restraints weight = 19193.737| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.30 r_work: 0.3048 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10096 Z= 0.107 Angle : 0.538 9.848 13653 Z= 0.256 Chirality : 0.041 0.134 1507 Planarity : 0.004 0.045 1793 Dihedral : 7.879 108.472 1442 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.19 % Allowed : 11.53 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.20 (0.25), residues: 1242 helix: 1.97 (0.22), residues: 596 sheet: 0.45 (0.43), residues: 153 loop : -0.53 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 338 TYR 0.006 0.001 TYR C 608 PHE 0.007 0.001 PHE A 363 TRP 0.007 0.001 TRP C 580 HIS 0.004 0.001 HIS C 633 Details of bonding type rmsd covalent geometry : bond 0.00246 (10096) covalent geometry : angle 0.53789 (13653) hydrogen bonds : bond 0.03571 ( 445) hydrogen bonds : angle 3.69422 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8728 (tm-30) REVERT: A 368 ASP cc_start: 0.8510 (t70) cc_final: 0.8185 (t70) REVERT: A 442 MET cc_start: 0.8981 (tmm) cc_final: 0.8715 (tmm) REVERT: A 450 ASP cc_start: 0.8831 (t0) cc_final: 0.8522 (t0) REVERT: B 335 LEU cc_start: 0.9080 (tp) cc_final: 0.8852 (tp) REVERT: B 556 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: B 599 ARG cc_start: 0.8828 (ptp-110) cc_final: 0.7478 (mmm160) REVERT: B 614 LYS cc_start: 0.4312 (tmtt) cc_final: 0.3343 (tmtt) REVERT: B 766 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.6435 (tpt170) REVERT: C 562 ARG cc_start: 0.6154 (mmt180) cc_final: 0.5865 (mmt180) REVERT: C 605 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: C 633 HIS cc_start: 0.9136 (OUTLIER) cc_final: 0.8535 (m170) REVERT: C 638 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8900 (m-80) REVERT: C 646 LYS cc_start: 0.9220 (ttmm) cc_final: 0.8922 (tmtt) outliers start: 23 outliers final: 13 residues processed: 182 average time/residue: 0.1072 time to fit residues: 26.0570 Evaluate side-chains 177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083823 restraints weight = 19290.165| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.28 r_work: 0.3036 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10096 Z= 0.122 Angle : 0.542 9.473 13653 Z= 0.259 Chirality : 0.041 0.134 1507 Planarity : 0.004 0.045 1793 Dihedral : 7.828 108.449 1442 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.53 % Allowed : 12.68 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.18 (0.25), residues: 1242 helix: 1.95 (0.22), residues: 598 sheet: 0.44 (0.43), residues: 153 loop : -0.56 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 338 TYR 0.007 0.001 TYR B 644 PHE 0.007 0.001 PHE A 771 TRP 0.005 0.001 TRP C 580 HIS 0.003 0.001 HIS C 633 Details of bonding type rmsd covalent geometry : bond 0.00288 (10096) covalent geometry : angle 0.54248 (13653) hydrogen bonds : bond 0.03587 ( 445) hydrogen bonds : angle 3.65801 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 368 ASP cc_start: 0.8519 (t70) cc_final: 0.8174 (t70) REVERT: A 442 MET cc_start: 0.8978 (tmm) cc_final: 0.8729 (tmm) REVERT: A 450 ASP cc_start: 0.8831 (t0) cc_final: 0.8526 (t0) REVERT: B 335 LEU cc_start: 0.9059 (tp) cc_final: 0.8816 (tp) REVERT: B 561 GLU cc_start: 0.8438 (pm20) cc_final: 0.8226 (mp0) REVERT: B 599 ARG cc_start: 0.8851 (ptp-110) cc_final: 0.7448 (mmm160) REVERT: B 614 LYS cc_start: 0.4352 (tmtt) cc_final: 0.2660 (tttp) REVERT: B 766 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.6317 (tpt170) REVERT: C 562 ARG cc_start: 0.6309 (mmt180) cc_final: 0.6029 (mmt180) REVERT: C 605 GLU cc_start: 0.8482 (tp30) cc_final: 0.7645 (mm-30) REVERT: C 633 HIS cc_start: 0.9124 (OUTLIER) cc_final: 0.8513 (m170) REVERT: C 638 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: C 646 LYS cc_start: 0.9224 (ttmm) cc_final: 0.8921 (tmtt) outliers start: 16 outliers final: 8 residues processed: 181 average time/residue: 0.1093 time to fit residues: 26.3575 Evaluate side-chains 170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.0870 chunk 50 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082874 restraints weight = 19418.598| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.30 r_work: 0.3019 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10096 Z= 0.153 Angle : 0.560 10.044 13653 Z= 0.268 Chirality : 0.042 0.136 1507 Planarity : 0.004 0.057 1793 Dihedral : 7.898 110.120 1440 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.19 % Allowed : 12.68 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.18 (0.25), residues: 1242 helix: 1.98 (0.22), residues: 591 sheet: 0.42 (0.44), residues: 153 loop : -0.55 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 338 TYR 0.008 0.001 TYR B 644 PHE 0.007 0.001 PHE B 768 TRP 0.004 0.001 TRP B 454 HIS 0.002 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00365 (10096) covalent geometry : angle 0.56026 (13653) hydrogen bonds : bond 0.03794 ( 445) hydrogen bonds : angle 3.70957 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8754 (tm-30) REVERT: A 368 ASP cc_start: 0.8498 (t70) cc_final: 0.7966 (t70) REVERT: A 442 MET cc_start: 0.8971 (tmm) cc_final: 0.8720 (tmm) REVERT: A 450 ASP cc_start: 0.8860 (t0) cc_final: 0.8556 (t0) REVERT: A 489 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9356 (mm) REVERT: B 335 LEU cc_start: 0.9009 (tp) cc_final: 0.8744 (tp) REVERT: B 501 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8606 (p0) REVERT: B 556 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: B 599 ARG cc_start: 0.8863 (ptp-110) cc_final: 0.7521 (mmm160) REVERT: B 614 LYS cc_start: 0.4422 (tmtt) cc_final: 0.2957 (tmtt) REVERT: B 766 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.6407 (tpt170) REVERT: C 562 ARG cc_start: 0.6336 (mmt180) cc_final: 0.5858 (mmt180) REVERT: C 632 LYS cc_start: 0.9432 (ttpt) cc_final: 0.9174 (ttpt) REVERT: C 633 HIS cc_start: 0.9112 (OUTLIER) cc_final: 0.8804 (m-70) REVERT: C 638 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8895 (m-80) REVERT: C 646 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8948 (tmtt) REVERT: C 654 GLN cc_start: 0.9203 (tt0) cc_final: 0.8935 (tm-30) outliers start: 23 outliers final: 11 residues processed: 180 average time/residue: 0.1132 time to fit residues: 27.1752 Evaluate side-chains 173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.0040 chunk 114 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.0040 chunk 122 optimal weight: 2.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.107833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.085250 restraints weight = 19096.044| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.26 r_work: 0.3068 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10096 Z= 0.098 Angle : 0.544 9.823 13653 Z= 0.258 Chirality : 0.041 0.131 1507 Planarity : 0.004 0.051 1793 Dihedral : 7.740 108.043 1440 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.53 % Allowed : 13.35 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.27 (0.25), residues: 1242 helix: 2.03 (0.22), residues: 599 sheet: 0.48 (0.44), residues: 153 loop : -0.50 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 338 TYR 0.006 0.001 TYR A 517 PHE 0.012 0.001 PHE B 360 TRP 0.006 0.001 TRP A 551 HIS 0.002 0.000 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00224 (10096) covalent geometry : angle 0.54399 (13653) hydrogen bonds : bond 0.03094 ( 445) hydrogen bonds : angle 3.50876 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8754 (tm-30) REVERT: A 368 ASP cc_start: 0.8486 (t70) cc_final: 0.8131 (t70) REVERT: A 442 MET cc_start: 0.8960 (tmm) cc_final: 0.8713 (tmm) REVERT: A 450 ASP cc_start: 0.8807 (t0) cc_final: 0.8507 (t0) REVERT: A 489 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9350 (mm) REVERT: B 335 LEU cc_start: 0.9032 (tp) cc_final: 0.8800 (tp) REVERT: B 417 GLU cc_start: 0.8961 (tp30) cc_final: 0.8730 (tp30) REVERT: B 501 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8581 (p0) REVERT: B 556 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: B 599 ARG cc_start: 0.8820 (ptp-110) cc_final: 0.7451 (mmm160) REVERT: B 614 LYS cc_start: 0.4315 (tmtt) cc_final: 0.2592 (tttp) REVERT: B 738 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 766 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.6374 (tpt170) REVERT: C 562 ARG cc_start: 0.6159 (mmt180) cc_final: 0.5955 (mmt180) REVERT: C 632 LYS cc_start: 0.9439 (ttpt) cc_final: 0.9098 (ttpt) REVERT: C 638 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: C 646 LYS cc_start: 0.9201 (ttmm) cc_final: 0.8918 (tmtt) outliers start: 16 outliers final: 9 residues processed: 184 average time/residue: 0.1173 time to fit residues: 28.9435 Evaluate side-chains 174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.0270 chunk 119 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.107610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.084914 restraints weight = 19089.340| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.27 r_work: 0.3062 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10096 Z= 0.107 Angle : 0.559 9.802 13653 Z= 0.265 Chirality : 0.041 0.133 1507 Planarity : 0.004 0.066 1793 Dihedral : 7.661 106.220 1440 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.43 % Allowed : 13.54 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.24 (0.25), residues: 1242 helix: 1.96 (0.22), residues: 601 sheet: 0.46 (0.44), residues: 153 loop : -0.47 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 338 TYR 0.006 0.001 TYR A 517 PHE 0.006 0.001 PHE A 771 TRP 0.004 0.001 TRP C 580 HIS 0.002 0.000 HIS C 633 Details of bonding type rmsd covalent geometry : bond 0.00253 (10096) covalent geometry : angle 0.55907 (13653) hydrogen bonds : bond 0.03176 ( 445) hydrogen bonds : angle 3.56641 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8782 (tm-30) REVERT: A 368 ASP cc_start: 0.8466 (t70) cc_final: 0.8114 (t70) REVERT: A 442 MET cc_start: 0.8956 (tmm) cc_final: 0.8710 (tmm) REVERT: A 450 ASP cc_start: 0.8829 (t0) cc_final: 0.8528 (t0) REVERT: A 489 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9339 (mm) REVERT: B 335 LEU cc_start: 0.9004 (tp) cc_final: 0.8771 (tp) REVERT: B 402 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: B 417 GLU cc_start: 0.8966 (tp30) cc_final: 0.8733 (tp30) REVERT: B 501 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8583 (p0) REVERT: B 556 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: B 558 ASN cc_start: 0.8900 (m-40) cc_final: 0.8513 (m-40) REVERT: B 599 ARG cc_start: 0.8828 (ptp-110) cc_final: 0.7484 (mmm160) REVERT: B 614 LYS cc_start: 0.4377 (tmtt) cc_final: 0.3039 (tttt) REVERT: B 738 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8637 (tm-30) REVERT: B 766 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.6339 (tpt170) REVERT: C 562 ARG cc_start: 0.6177 (mmt180) cc_final: 0.5843 (mmt180) REVERT: C 566 ARG cc_start: 0.8574 (mmm160) cc_final: 0.8258 (mmm160) REVERT: C 586 ASP cc_start: 0.8228 (m-30) cc_final: 0.8006 (m-30) REVERT: C 632 LYS cc_start: 0.9448 (ttpt) cc_final: 0.9133 (tmmt) REVERT: C 633 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8865 (m-70) REVERT: C 638 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: C 646 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8930 (tmtt) REVERT: C 654 GLN cc_start: 0.9197 (tt0) cc_final: 0.8949 (tm-30) outliers start: 15 outliers final: 7 residues processed: 175 average time/residue: 0.1189 time to fit residues: 27.9108 Evaluate side-chains 175 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.107899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085099 restraints weight = 19258.148| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.29 r_work: 0.3059 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10096 Z= 0.112 Angle : 0.572 9.720 13653 Z= 0.272 Chirality : 0.042 0.131 1507 Planarity : 0.004 0.059 1793 Dihedral : 7.633 104.921 1440 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.62 % Allowed : 13.35 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.29 (0.25), residues: 1242 helix: 2.03 (0.22), residues: 595 sheet: 0.49 (0.44), residues: 153 loop : -0.46 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 338 TYR 0.006 0.001 TYR A 517 PHE 0.006 0.001 PHE A 771 TRP 0.005 0.001 TRP C 580 HIS 0.002 0.000 HIS C 633 Details of bonding type rmsd covalent geometry : bond 0.00265 (10096) covalent geometry : angle 0.57163 (13653) hydrogen bonds : bond 0.03169 ( 445) hydrogen bonds : angle 3.55572 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8776 (tm-30) REVERT: A 368 ASP cc_start: 0.8453 (t70) cc_final: 0.8099 (t70) REVERT: A 442 MET cc_start: 0.8953 (tmm) cc_final: 0.8710 (tmm) REVERT: A 450 ASP cc_start: 0.8838 (t0) cc_final: 0.8538 (t0) REVERT: A 489 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9340 (mm) REVERT: B 335 LEU cc_start: 0.9016 (tp) cc_final: 0.8790 (tp) REVERT: B 402 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: B 417 GLU cc_start: 0.8967 (tp30) cc_final: 0.8735 (tp30) REVERT: B 501 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8584 (p0) REVERT: B 556 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: B 558 ASN cc_start: 0.8763 (m-40) cc_final: 0.8393 (m-40) REVERT: B 599 ARG cc_start: 0.8834 (ptp-110) cc_final: 0.7492 (mmm160) REVERT: B 614 LYS cc_start: 0.4366 (tmtt) cc_final: 0.2694 (tttt) REVERT: B 738 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8654 (tm-30) REVERT: B 766 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.6328 (tpt170) REVERT: C 562 ARG cc_start: 0.6068 (mmt180) cc_final: 0.5702 (mmt180) REVERT: C 566 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8253 (mmm160) REVERT: C 632 LYS cc_start: 0.9458 (ttpt) cc_final: 0.9188 (tmmt) REVERT: C 633 HIS cc_start: 0.9139 (OUTLIER) cc_final: 0.8881 (m-70) REVERT: C 638 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: C 646 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8947 (tmtt) outliers start: 17 outliers final: 9 residues processed: 176 average time/residue: 0.1149 time to fit residues: 27.0369 Evaluate side-chains 179 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 114 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.107867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084719 restraints weight = 19505.482| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.35 r_work: 0.3058 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10096 Z= 0.115 Angle : 0.580 9.789 13653 Z= 0.277 Chirality : 0.042 0.131 1507 Planarity : 0.004 0.105 1793 Dihedral : 7.635 103.486 1440 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.62 % Allowed : 13.44 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.31 (0.25), residues: 1242 helix: 2.05 (0.22), residues: 595 sheet: 0.48 (0.44), residues: 153 loop : -0.45 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 338 TYR 0.008 0.001 TYR C 608 PHE 0.006 0.001 PHE A 771 TRP 0.006 0.001 TRP C 580 HIS 0.002 0.000 HIS C 633 Details of bonding type rmsd covalent geometry : bond 0.00274 (10096) covalent geometry : angle 0.58038 (13653) hydrogen bonds : bond 0.03188 ( 445) hydrogen bonds : angle 3.55496 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8781 (tm-30) REVERT: A 368 ASP cc_start: 0.8427 (t70) cc_final: 0.8068 (t70) REVERT: A 450 ASP cc_start: 0.8844 (t0) cc_final: 0.8550 (t0) REVERT: A 489 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9341 (mm) REVERT: B 402 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: B 417 GLU cc_start: 0.8972 (tp30) cc_final: 0.8743 (tp30) REVERT: B 501 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8586 (p0) REVERT: B 556 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: B 599 ARG cc_start: 0.8820 (ptp-110) cc_final: 0.7332 (mmm-85) REVERT: B 614 LYS cc_start: 0.4367 (tmtt) cc_final: 0.2702 (tttt) REVERT: B 738 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 766 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.6328 (tpt170) REVERT: C 566 ARG cc_start: 0.8573 (mmm160) cc_final: 0.8280 (mmm160) REVERT: C 585 TYR cc_start: 0.8752 (m-10) cc_final: 0.8437 (m-10) REVERT: C 605 GLU cc_start: 0.8430 (tp30) cc_final: 0.7916 (mm-30) REVERT: C 632 LYS cc_start: 0.9461 (ttpt) cc_final: 0.9151 (tmmt) REVERT: C 633 HIS cc_start: 0.9119 (OUTLIER) cc_final: 0.8652 (m-70) REVERT: C 638 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: C 646 LYS cc_start: 0.9225 (ttmm) cc_final: 0.8960 (tmtt) REVERT: C 654 GLN cc_start: 0.9182 (tt0) cc_final: 0.8922 (tm-30) outliers start: 17 outliers final: 9 residues processed: 176 average time/residue: 0.1192 time to fit residues: 27.9019 Evaluate side-chains 177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 638 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.107447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084777 restraints weight = 19182.132| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.27 r_work: 0.3058 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10096 Z= 0.117 Angle : 0.601 11.107 13653 Z= 0.283 Chirality : 0.042 0.131 1507 Planarity : 0.004 0.086 1793 Dihedral : 7.627 102.046 1440 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.53 % Allowed : 13.73 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 aren not related in a simple way. whole: 1.32 (0.25), residues: 1242 helix: 2.07 (0.22), residues: 595 sheet: 0.49 (0.44), residues: 153 loop : -0.46 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 338 TYR 0.016 0.001 TYR C 612 PHE 0.006 0.001 PHE A 771 TRP 0.004 0.001 TRP C 580 HIS 0.002 0.000 HIS C 633 Details of bonding type rmsd covalent geometry : bond 0.00277 (10096) covalent geometry : angle 0.60064 (13653) hydrogen bonds : bond 0.03197 ( 445) hydrogen bonds : angle 3.54273 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.55 seconds wall clock time: 37 minutes 42.95 seconds (2262.95 seconds total)