Starting phenix.real_space_refine on Wed Apr 30 21:34:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mq6_48514/04_2025/9mq6_48514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mq6_48514/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mq6_48514/04_2025/9mq6_48514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mq6_48514/04_2025/9mq6_48514.map" model { file = "/net/cci-nas-00/data/ceres_data/9mq6_48514/04_2025/9mq6_48514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mq6_48514/04_2025/9mq6_48514.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.07, per 1000 atoms: 0.71 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.16 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: 2.98 Time building geometry restraints manager: 3.08 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: 3.470 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.480 Find NCS groups from input model: 0.370 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (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 TRP 0.006 0.001 TRP B 454 HIS 0.002 0.001 HIS B 404 PHE 0.007 0.001 PHE B 758 TYR 0.007 0.001 TYR B 644 ARG 0.003 0.000 ARG B 653 Details of bonding type rmsd hydrogen bonds : bond 0.18675 ( 445) hydrogen bonds : angle 5.99050 ( 1272) covalent geometry : bond 0.00269 (10096) covalent geometry : angle 0.47492 (13653) *********************** 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 : 1.063 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: 0.3084 time to fit residues: 90.3226 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 : 1.033 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087016 restraints weight = 19051.857| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.17 r_work: 0.3087 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10096 Z= 0.120 Angle : 0.568 8.366 13653 Z= 0.279 Chirality : 0.042 0.144 1507 Planarity : 0.004 0.044 1793 Dihedral : 7.810 101.465 1442 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.53 % Allowed : 9.91 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1242 helix: 1.81 (0.22), residues: 584 sheet: 0.61 (0.44), residues: 150 loop : -0.39 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 580 HIS 0.006 0.001 HIS C 633 PHE 0.009 0.001 PHE A 736 TYR 0.010 0.001 TYR C 612 ARG 0.008 0.001 ARG B 708 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 445) hydrogen bonds : angle 4.11419 ( 1272) covalent geometry : bond 0.00266 (10096) covalent geometry : angle 0.56816 (13653) *********************** 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 193 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8672 (tm-30) REVERT: A 368 ASP cc_start: 0.8484 (t70) cc_final: 0.7991 (t70) REVERT: A 442 MET cc_start: 0.8941 (tmm) cc_final: 0.8690 (tmm) REVERT: A 450 ASP cc_start: 0.8862 (t0) cc_final: 0.8546 (t0) REVERT: A 663 LYS cc_start: 0.6190 (tttt) cc_final: 0.5843 (tttt) REVERT: A 742 PHE cc_start: 0.8491 (m-80) cc_final: 0.8230 (m-10) REVERT: B 218 GLU cc_start: 0.8358 (tt0) cc_final: 0.8127 (mt-10) REVERT: B 556 GLU cc_start: 0.8744 (mp0) cc_final: 0.8420 (mp0) REVERT: B 599 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.7326 (mmm-85) REVERT: B 614 LYS cc_start: 0.4474 (tmtt) cc_final: 0.3070 (tttm) REVERT: B 738 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 766 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.6441 (tpt170) REVERT: C 557 TYR cc_start: 0.7201 (m-80) cc_final: 0.6847 (m-80) REVERT: C 562 ARG cc_start: 0.6333 (mmt180) cc_final: 0.5868 (mmt180) REVERT: C 646 LYS cc_start: 0.9233 (ttmm) cc_final: 0.8964 (tmtt) REVERT: C 654 GLN cc_start: 0.9156 (tt0) cc_final: 0.8837 (pp30) outliers start: 16 outliers final: 8 residues processed: 184 average time/residue: 0.2426 time to fit residues: 60.5038 Evaluate side-chains 168 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 606 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 558 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 0.0470 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3597 r_free = 0.3597 target = 0.108305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085583 restraints weight = 19131.073| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.23 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: 0.8698 moved from start: 0.2086 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 : 0.534 8.286 13653 Z= 0.256 Chirality : 0.041 0.135 1507 Planarity : 0.004 0.051 1793 Dihedral : 7.602 100.715 1440 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.81 % Allowed : 10.10 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1242 helix: 2.00 (0.22), residues: 586 sheet: 0.61 (0.44), residues: 153 loop : -0.44 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 580 HIS 0.002 0.001 HIS B 499 PHE 0.006 0.001 PHE B 302 TYR 0.006 0.001 TYR C 608 ARG 0.007 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 445) hydrogen bonds : angle 3.79128 ( 1272) covalent geometry : bond 0.00244 (10096) covalent geometry : angle 0.53387 (13653) *********************** 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 180 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8707 (tm-30) REVERT: A 368 ASP cc_start: 0.8446 (t70) cc_final: 0.8130 (t70) REVERT: A 442 MET cc_start: 0.8980 (tmm) cc_final: 0.8707 (tmm) REVERT: A 450 ASP cc_start: 0.8795 (t0) cc_final: 0.8487 (t0) REVERT: B 599 ARG cc_start: 0.8826 (ptp-110) cc_final: 0.7427 (mmm160) REVERT: B 614 LYS cc_start: 0.4336 (tmtt) cc_final: 0.3338 (tttt) REVERT: B 738 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8575 (tm-30) REVERT: B 766 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.6365 (tpt170) REVERT: C 562 ARG cc_start: 0.6133 (mmt180) cc_final: 0.5872 (mmt180) REVERT: C 605 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7756 (mm-30) REVERT: C 646 LYS cc_start: 0.9210 (ttmm) cc_final: 0.8936 (tmtt) outliers start: 19 outliers final: 12 residues processed: 173 average time/residue: 0.2495 time to fit residues: 58.3966 Evaluate side-chains 169 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 558 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 45 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.109163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086565 restraints weight = 18900.248| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.22 r_work: 0.3087 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10096 Z= 0.097 Angle : 0.525 10.024 13653 Z= 0.249 Chirality : 0.041 0.132 1507 Planarity : 0.004 0.043 1793 Dihedral : 7.453 99.103 1440 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.81 % Allowed : 10.96 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1242 helix: 2.12 (0.22), residues: 586 sheet: 0.52 (0.43), residues: 153 loop : -0.42 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 598 HIS 0.002 0.000 HIS C 578 PHE 0.006 0.001 PHE B 302 TYR 0.006 0.001 TYR C 608 ARG 0.006 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 445) hydrogen bonds : angle 3.57345 ( 1272) covalent geometry : bond 0.00220 (10096) covalent geometry : angle 0.52487 (13653) *********************** 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 195 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8698 (tm-30) REVERT: A 368 ASP cc_start: 0.8419 (t70) cc_final: 0.8092 (t70) REVERT: A 442 MET cc_start: 0.8969 (tmm) cc_final: 0.8725 (tmm) REVERT: A 450 ASP cc_start: 0.8814 (t0) cc_final: 0.8502 (t0) REVERT: B 417 GLU cc_start: 0.8951 (tp30) cc_final: 0.8704 (tp30) REVERT: B 599 ARG cc_start: 0.8788 (ptp-110) cc_final: 0.7357 (mmm160) REVERT: B 614 LYS cc_start: 0.4344 (tmtt) cc_final: 0.3088 (tttt) REVERT: B 738 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 766 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.6375 (tpt170) REVERT: C 562 ARG cc_start: 0.6180 (mmt180) cc_final: 0.5858 (mmt180) REVERT: C 566 ARG cc_start: 0.8479 (mmm160) cc_final: 0.8069 (mmm160) REVERT: C 633 HIS cc_start: 0.9135 (OUTLIER) cc_final: 0.8752 (m90) REVERT: C 646 LYS cc_start: 0.9194 (ttmm) cc_final: 0.8905 (tmtt) REVERT: C 654 GLN cc_start: 0.9147 (tt0) cc_final: 0.8896 (tm-30) outliers start: 19 outliers final: 10 residues processed: 185 average time/residue: 0.2853 time to fit residues: 71.1165 Evaluate side-chains 174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 695 CYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 104 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.108662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085974 restraints weight = 18994.550| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.27 r_work: 0.3079 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10096 Z= 0.103 Angle : 0.538 10.240 13653 Z= 0.255 Chirality : 0.041 0.132 1507 Planarity : 0.004 0.050 1793 Dihedral : 7.378 98.588 1438 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.43 % Allowed : 11.53 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1242 helix: 2.16 (0.22), residues: 588 sheet: 0.52 (0.43), residues: 153 loop : -0.42 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 598 HIS 0.002 0.000 HIS C 578 PHE 0.006 0.001 PHE A 771 TYR 0.037 0.001 TYR A 203 ARG 0.010 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 445) hydrogen bonds : angle 3.51089 ( 1272) covalent geometry : bond 0.00238 (10096) covalent geometry : angle 0.53759 (13653) *********************** 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 186 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8427 (t70) cc_final: 0.8080 (t70) REVERT: A 442 MET cc_start: 0.8965 (tmm) cc_final: 0.8719 (tmm) REVERT: A 450 ASP cc_start: 0.8808 (t0) cc_final: 0.8498 (t0) REVERT: B 417 GLU cc_start: 0.8963 (tp30) cc_final: 0.8709 (tp30) REVERT: B 599 ARG cc_start: 0.8789 (ptp-110) cc_final: 0.7284 (mmm160) REVERT: B 614 LYS cc_start: 0.4354 (tmtt) cc_final: 0.3038 (tttt) REVERT: B 738 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8658 (tm-30) REVERT: B 766 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.6370 (tpt170) REVERT: C 562 ARG cc_start: 0.6325 (mmt180) cc_final: 0.6111 (mmt180) REVERT: C 566 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8060 (mmm160) REVERT: C 604 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7300 (tpt-90) REVERT: C 605 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8036 (tt0) REVERT: C 632 LYS cc_start: 0.9589 (ttpt) cc_final: 0.8959 (ttpt) REVERT: C 633 HIS cc_start: 0.9111 (OUTLIER) cc_final: 0.8389 (m90) REVERT: C 646 LYS cc_start: 0.9193 (ttmm) cc_final: 0.8899 (tmtt) outliers start: 15 outliers final: 8 residues processed: 178 average time/residue: 0.2987 time to fit residues: 70.5187 Evaluate side-chains 173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 367 VAL Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085208 restraints weight = 19197.120| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.29 r_work: 0.3063 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2508 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= 0.112 Angle : 0.544 9.931 13653 Z= 0.258 Chirality : 0.041 0.133 1507 Planarity : 0.004 0.059 1793 Dihedral : 7.354 98.184 1438 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.72 % Allowed : 11.73 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1242 helix: 2.17 (0.22), residues: 588 sheet: 0.50 (0.43), residues: 153 loop : -0.45 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 580 HIS 0.002 0.001 HIS A 226 PHE 0.007 0.001 PHE A 771 TYR 0.026 0.001 TYR A 203 ARG 0.012 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 445) hydrogen bonds : angle 3.50599 ( 1272) covalent geometry : bond 0.00264 (10096) covalent geometry : angle 0.54378 (13653) *********************** 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 186 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8752 (tm-30) REVERT: A 368 ASP cc_start: 0.8424 (t70) cc_final: 0.8078 (t70) REVERT: A 442 MET cc_start: 0.8971 (tmm) cc_final: 0.8732 (tmm) REVERT: A 450 ASP cc_start: 0.8820 (t0) cc_final: 0.8512 (t0) REVERT: B 501 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8567 (p0) REVERT: B 599 ARG cc_start: 0.8822 (ptp-110) cc_final: 0.7387 (mmm160) REVERT: B 614 LYS cc_start: 0.4378 (tmtt) cc_final: 0.3147 (tttt) REVERT: B 766 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.6303 (tpt170) REVERT: C 562 ARG cc_start: 0.6337 (mmt180) cc_final: 0.6126 (mmt180) REVERT: C 566 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8131 (mmm160) REVERT: C 604 ARG cc_start: 0.7658 (mmm160) cc_final: 0.7309 (tpt-90) REVERT: C 632 LYS cc_start: 0.9592 (ttpt) cc_final: 0.9333 (tmmt) REVERT: C 633 HIS cc_start: 0.9105 (OUTLIER) cc_final: 0.8812 (m90) REVERT: C 646 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8922 (tmtt) REVERT: C 654 GLN cc_start: 0.9148 (tt0) cc_final: 0.8908 (tm-30) outliers start: 18 outliers final: 11 residues processed: 178 average time/residue: 0.2760 time to fit residues: 65.8020 Evaluate side-chains 176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 633 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 67 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 99 optimal weight: 0.0970 chunk 109 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.109121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086257 restraints weight = 19323.559| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.33 r_work: 0.3079 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10096 Z= 0.098 Angle : 0.538 9.581 13653 Z= 0.254 Chirality : 0.041 0.131 1507 Planarity : 0.004 0.067 1793 Dihedral : 7.284 97.044 1438 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.43 % Allowed : 12.68 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1242 helix: 2.19 (0.22), residues: 588 sheet: 0.48 (0.43), residues: 153 loop : -0.45 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 580 HIS 0.002 0.000 HIS C 633 PHE 0.007 0.001 PHE A 771 TYR 0.020 0.001 TYR A 203 ARG 0.014 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 445) hydrogen bonds : angle 3.43149 ( 1272) covalent geometry : bond 0.00228 (10096) covalent geometry : angle 0.53752 (13653) *********************** 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 187 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8780 (tm-30) REVERT: A 368 ASP cc_start: 0.8386 (t70) cc_final: 0.8039 (t70) REVERT: A 442 MET cc_start: 0.8967 (tmm) cc_final: 0.8731 (tmm) REVERT: A 450 ASP cc_start: 0.8829 (t0) cc_final: 0.8521 (t0) REVERT: B 349 ARG cc_start: 0.8681 (pmt170) cc_final: 0.8365 (ttp80) REVERT: B 359 ARG cc_start: 0.8805 (mmt90) cc_final: 0.7636 (mtp180) REVERT: B 417 GLU cc_start: 0.8959 (tp30) cc_final: 0.8701 (tp30) REVERT: B 501 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8581 (p0) REVERT: B 599 ARG cc_start: 0.8813 (ptp-110) cc_final: 0.7344 (mmm160) REVERT: B 614 LYS cc_start: 0.4466 (tmtt) cc_final: 0.3240 (tttt) REVERT: B 766 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.6264 (tpt170) REVERT: C 566 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8111 (mmm160) REVERT: C 633 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8741 (m90) REVERT: C 646 LYS cc_start: 0.9197 (ttmm) cc_final: 0.8906 (tmtt) outliers start: 15 outliers final: 11 residues processed: 180 average time/residue: 0.2720 time to fit residues: 65.9030 Evaluate side-chains 182 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 695 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 0.0070 chunk 121 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 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 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3616 r_free = 0.3616 target = 0.109465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086200 restraints weight = 19540.882| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.39 r_work: 0.3078 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 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 : 0.002 0.037 10096 Z= 0.099 Angle : 0.555 9.893 13653 Z= 0.259 Chirality : 0.041 0.131 1507 Planarity : 0.004 0.044 1793 Dihedral : 7.201 96.540 1438 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.43 % Allowed : 13.06 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1242 helix: 2.22 (0.22), residues: 588 sheet: 0.39 (0.43), residues: 154 loop : -0.44 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 580 HIS 0.003 0.000 HIS C 633 PHE 0.007 0.001 PHE A 771 TYR 0.018 0.001 TYR A 203 ARG 0.007 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 445) hydrogen bonds : angle 3.39690 ( 1272) covalent geometry : bond 0.00231 (10096) covalent geometry : angle 0.55469 (13653) *********************** 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 190 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8794 (tm-30) REVERT: A 368 ASP cc_start: 0.8378 (t70) cc_final: 0.8158 (t0) REVERT: A 442 MET cc_start: 0.8966 (tmm) cc_final: 0.8730 (tmm) REVERT: A 450 ASP cc_start: 0.8823 (t0) cc_final: 0.8519 (t0) REVERT: B 349 ARG cc_start: 0.8686 (pmt170) cc_final: 0.8374 (ttp80) REVERT: B 417 GLU cc_start: 0.8961 (tp30) cc_final: 0.8699 (tp30) REVERT: B 501 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8581 (p0) REVERT: B 599 ARG cc_start: 0.8806 (ptp-110) cc_final: 0.7319 (mmm160) REVERT: B 614 LYS cc_start: 0.4546 (tmtt) cc_final: 0.3293 (tttt) REVERT: B 766 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.6245 (tpt170) REVERT: C 566 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8162 (mmm160) REVERT: C 604 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7447 (tpt-90) REVERT: C 632 LYS cc_start: 0.9596 (tmmt) cc_final: 0.9386 (ttpt) REVERT: C 633 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8756 (m90) REVERT: C 646 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8939 (tmtt) outliers start: 15 outliers final: 9 residues processed: 182 average time/residue: 0.2619 time to fit residues: 63.5815 Evaluate side-chains 177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 695 CYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 109 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.109679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086997 restraints weight = 19219.789| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.25 r_work: 0.3094 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10096 Z= 0.101 Angle : 0.571 9.503 13653 Z= 0.269 Chirality : 0.041 0.131 1507 Planarity : 0.004 0.080 1793 Dihedral : 7.144 95.925 1438 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.24 % Allowed : 13.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1242 helix: 2.24 (0.22), residues: 588 sheet: 0.41 (0.43), residues: 154 loop : -0.47 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 580 HIS 0.003 0.000 HIS C 633 PHE 0.007 0.001 PHE A 771 TYR 0.016 0.001 TYR A 203 ARG 0.019 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 445) hydrogen bonds : angle 3.39248 ( 1272) covalent geometry : bond 0.00236 (10096) covalent geometry : angle 0.57085 (13653) *********************** 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 186 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8778 (tm-30) REVERT: A 368 ASP cc_start: 0.8309 (t70) cc_final: 0.8104 (t0) REVERT: A 442 MET cc_start: 0.8945 (tmm) cc_final: 0.8715 (tmm) REVERT: A 450 ASP cc_start: 0.8816 (t0) cc_final: 0.8508 (t0) REVERT: B 349 ARG cc_start: 0.8679 (pmt170) cc_final: 0.8380 (ttp80) REVERT: B 359 ARG cc_start: 0.8809 (mmt90) cc_final: 0.7635 (mtp180) REVERT: B 402 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: B 417 GLU cc_start: 0.8950 (tp30) cc_final: 0.8688 (tp30) REVERT: B 501 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8548 (p0) REVERT: B 599 ARG cc_start: 0.8793 (ptp-110) cc_final: 0.7314 (mmm160) REVERT: B 614 LYS cc_start: 0.4544 (tmtt) cc_final: 0.3213 (tttt) REVERT: B 766 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.6238 (tpt170) REVERT: C 562 ARG cc_start: 0.6405 (mmt180) cc_final: 0.6180 (mmt180) REVERT: C 566 ARG cc_start: 0.8569 (mmm160) cc_final: 0.8207 (mmm160) REVERT: C 604 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7392 (tpt-90) REVERT: C 632 LYS cc_start: 0.9602 (tmmt) cc_final: 0.9369 (ttpt) REVERT: C 633 HIS cc_start: 0.9130 (OUTLIER) cc_final: 0.8762 (m90) REVERT: C 646 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8946 (tmtt) outliers start: 13 outliers final: 10 residues processed: 178 average time/residue: 0.2625 time to fit residues: 62.3248 Evaluate side-chains 181 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 435 GLU 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 456 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 5 optimal weight: 0.0030 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.110645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087451 restraints weight = 19532.041| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.40 r_work: 0.3097 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10096 Z= 0.098 Angle : 0.576 9.868 13653 Z= 0.272 Chirality : 0.041 0.131 1507 Planarity : 0.004 0.074 1793 Dihedral : 7.065 95.240 1438 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.24 % Allowed : 13.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1242 helix: 2.23 (0.22), residues: 587 sheet: 0.44 (0.43), residues: 154 loop : -0.47 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 580 HIS 0.003 0.000 HIS C 633 PHE 0.009 0.001 PHE B 363 TYR 0.015 0.001 TYR A 203 ARG 0.016 0.001 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.02740 ( 445) hydrogen bonds : angle 3.37094 ( 1272) covalent geometry : bond 0.00227 (10096) covalent geometry : angle 0.57625 (13653) ********************** 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 194 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 288 LYS cc_start: 0.9240 (ttmm) cc_final: 0.8883 (tppt) REVERT: A 368 ASP cc_start: 0.8322 (t70) cc_final: 0.8114 (t0) REVERT: A 442 MET cc_start: 0.8946 (tmm) cc_final: 0.8708 (tmm) REVERT: A 450 ASP cc_start: 0.8821 (t0) cc_final: 0.8516 (t0) REVERT: B 349 ARG cc_start: 0.8689 (pmt170) cc_final: 0.8400 (ttp80) REVERT: B 359 ARG cc_start: 0.8805 (mmt90) cc_final: 0.7586 (mtp180) REVERT: B 402 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 417 GLU cc_start: 0.8952 (tp30) cc_final: 0.8692 (tp30) REVERT: B 501 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8558 (p0) REVERT: B 599 ARG cc_start: 0.8794 (ptp-110) cc_final: 0.7296 (mmm160) REVERT: B 614 LYS cc_start: 0.4504 (tmtt) cc_final: 0.3168 (tttt) REVERT: B 766 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.6234 (tpt170) REVERT: C 562 ARG cc_start: 0.6416 (mmt180) cc_final: 0.6207 (mmt180) REVERT: C 566 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8190 (mmm160) REVERT: C 632 LYS cc_start: 0.9609 (tmmt) cc_final: 0.9405 (ttpt) REVERT: C 633 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8802 (m90) REVERT: C 646 LYS cc_start: 0.9206 (ttmm) cc_final: 0.8941 (tmtt) outliers start: 13 outliers final: 9 residues processed: 186 average time/residue: 0.2685 time to fit residues: 66.3640 Evaluate side-chains 185 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 367 VAL Chi-restraints excluded: chain A residue 435 GLU 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 456 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 633 HIS 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 49 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** C 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.106446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083562 restraints weight = 19399.462| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.30 r_work: 0.3032 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10096 Z= 0.174 Angle : 0.635 9.703 13653 Z= 0.304 Chirality : 0.043 0.139 1507 Planarity : 0.004 0.073 1793 Dihedral : 7.300 97.956 1438 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.14 % Allowed : 13.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1242 helix: 2.12 (0.22), residues: 588 sheet: 0.41 (0.43), residues: 153 loop : -0.56 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 454 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE B 360 TYR 0.017 0.001 TYR A 203 ARG 0.015 0.001 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 445) hydrogen bonds : angle 3.64281 ( 1272) covalent geometry : bond 0.00419 (10096) covalent geometry : angle 0.63537 (13653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4904.96 seconds wall clock time: 86 minutes 24.93 seconds (5184.93 seconds total)