Starting phenix.real_space_refine on Tue Feb 3 22:01:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n86_49116/02_2026/9n86_49116.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n86_49116/02_2026/9n86_49116.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/9n86_49116/02_2026/9n86_49116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n86_49116/02_2026/9n86_49116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n86_49116/02_2026/9n86_49116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n86_49116/02_2026/9n86_49116.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= 0.001 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4507 2.51 5 N 1224 2.21 5 O 1393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7173 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6805 Classifications: {'peptide': 876} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 838} Chain: "B" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 368 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Time building chain proxies: 1.36, per 1000 atoms: 0.19 Number of scatterers: 7173 At special positions: 0 Unit cell: (89.54, 90.28, 111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1393 8.00 N 1224 7.00 C 4507 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: 0.54 Conformation dependent library (CDL) restraints added in 232.6 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 84.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.909A pdb=" N ILE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 31 removed outlier: 3.517A pdb=" N GLU A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 50 through 66 removed outlier: 3.864A pdb=" N LEU A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.836A pdb=" N VAL A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.757A pdb=" N CYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.534A pdb=" N GLN A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.702A pdb=" N THR A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.659A pdb=" N ASN A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 211 through 227 removed outlier: 3.506A pdb=" N VAL A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 removed outlier: 3.634A pdb=" N ARG A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.799A pdb=" N GLU A 253 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 254 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.711A pdb=" N ALA A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 303 removed outlier: 3.933A pdb=" N CYS A 287 " --> pdb=" O TRP A 283 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 318 through 330 Proline residue: A 324 - end of helix removed outlier: 3.509A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.756A pdb=" N MET A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.534A pdb=" N GLY A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 392 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 417 removed outlier: 3.696A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Proline residue: A 404 - end of helix Proline residue: A 411 - end of helix removed outlier: 3.854A pdb=" N GLU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.741A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 removed outlier: 4.436A pdb=" N ALA A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.582A pdb=" N LEU A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 485 removed outlier: 4.560A pdb=" N ASN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 473 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 4.318A pdb=" N SER A 501 " --> pdb=" O CYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 removed outlier: 3.849A pdb=" N ASP A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 538 Processing helix chain 'A' and resid 543 through 567 removed outlier: 3.843A pdb=" N GLN A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 Processing helix chain 'A' and resid 596 through 617 removed outlier: 3.673A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.248A pdb=" N GLN A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.635A pdb=" N LYS A 645 " --> pdb=" O GLU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 659 Proline residue: A 652 - end of helix Processing helix chain 'A' and resid 663 through 681 removed outlier: 3.591A pdb=" N GLY A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 702 removed outlier: 4.388A pdb=" N ASP A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 725 removed outlier: 4.472A pdb=" N GLN A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 4.143A pdb=" N LYS A 729 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 730 " --> pdb=" O GLU A 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 730' Processing helix chain 'A' and resid 731 through 744 Processing helix chain 'A' and resid 751 through 778 removed outlier: 3.579A pdb=" N LEU A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 792 removed outlier: 3.654A pdb=" N VAL A 790 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Proline residue: A 792 - end of helix Processing helix chain 'A' and resid 793 through 807 Processing helix chain 'A' and resid 811 through 829 removed outlier: 3.922A pdb=" N VAL A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 816 " --> pdb=" O ASP A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 840 removed outlier: 3.958A pdb=" N LEU A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 836 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 853 removed outlier: 4.030A pdb=" N ARG A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 874 removed outlier: 3.613A pdb=" N LEU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 23 through 51 481 hydrogen bonds defined for protein. 1419 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: 0.83 Time building geometry restraints manager: 0.73 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: 2434 1.34 - 1.46: 1109 1.46 - 1.58: 3667 1.58 - 1.70: 0 1.70 - 1.81: 75 Bond restraints: 7285 Sorted by residual: bond pdb=" CB MET A 555 " pdb=" CG MET A 555 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CB GLN B 46 " pdb=" CG GLN B 46 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CA THR A 254 " pdb=" CB THR A 254 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.41e-02 5.03e+03 1.01e+00 bond pdb=" CB THR A 254 " pdb=" CG2 THR A 254 " ideal model delta sigma weight residual 1.521 1.552 -0.031 3.30e-02 9.18e+02 8.68e-01 bond pdb=" CB MET A 842 " pdb=" CG MET A 842 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.57e-01 ... (remaining 7280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 9764 2.27 - 4.53: 76 4.53 - 6.80: 31 6.80 - 9.06: 3 9.06 - 11.33: 1 Bond angle restraints: 9875 Sorted by residual: angle pdb=" CB MET A 555 " pdb=" CG MET A 555 " pdb=" SD MET A 555 " ideal model delta sigma weight residual 112.70 124.03 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" N VAL A 466 " pdb=" CA VAL A 466 " pdb=" C VAL A 466 " ideal model delta sigma weight residual 112.96 109.33 3.63 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA GLN B 46 " pdb=" CB GLN B 46 " pdb=" CG GLN B 46 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CB GLN B 46 " pdb=" CG GLN B 46 " pdb=" CD GLN B 46 " ideal model delta sigma weight residual 112.60 117.96 -5.36 1.70e+00 3.46e-01 9.95e+00 angle pdb=" CA MET A 555 " pdb=" CB MET A 555 " pdb=" CG MET A 555 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.36e+00 ... (remaining 9870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3744 17.91 - 35.82: 542 35.82 - 53.73: 177 53.73 - 71.64: 36 71.64 - 89.55: 11 Dihedral angle restraints: 4510 sinusoidal: 1810 harmonic: 2700 Sorted by residual: dihedral pdb=" CA ASP A 384 " pdb=" CB ASP A 384 " pdb=" CG ASP A 384 " pdb=" OD1 ASP A 384 " ideal model delta sinusoidal sigma weight residual -30.00 -87.53 57.53 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CG ARG B 39 " pdb=" CD ARG B 39 " pdb=" NE ARG B 39 " pdb=" CZ ARG B 39 " ideal model delta sinusoidal sigma weight residual 180.00 135.04 44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CB GLU A 203 " pdb=" CG GLU A 203 " pdb=" CD GLU A 203 " pdb=" OE1 GLU A 203 " ideal model delta sinusoidal sigma weight residual 0.00 87.75 -87.75 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 4507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1043 0.062 - 0.123: 101 0.123 - 0.185: 3 0.185 - 0.247: 0 0.247 - 0.308: 1 Chirality restraints: 1148 Sorted by residual: chirality pdb=" CB THR A 254 " pdb=" CA THR A 254 " pdb=" OG1 THR A 254 " pdb=" CG2 THR A 254 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CG LEU A 825 " pdb=" CB LEU A 825 " pdb=" CD1 LEU A 825 " pdb=" CD2 LEU A 825 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA VAL A 364 " pdb=" N VAL A 364 " pdb=" C VAL A 364 " pdb=" CB VAL A 364 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1145 not shown) Planarity restraints: 1291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 784 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 785 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 785 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 785 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 396 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 397 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 397 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 397 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 257 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 258 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.018 5.00e-02 4.00e+02 ... (remaining 1288 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 3728 2.99 - 3.47: 8564 3.47 - 3.95: 11257 3.95 - 4.42: 13070 4.42 - 4.90: 19693 Nonbonded interactions: 56312 Sorted by model distance: nonbonded pdb=" N THR A 770 " pdb=" OG1 THR A 770 " model vdw 2.517 2.496 nonbonded pdb=" N ASP B 45 " pdb=" OD1 ASP B 45 " model vdw 2.528 3.120 nonbonded pdb=" N ASP A 832 " pdb=" OD1 ASP A 832 " model vdw 2.567 3.120 nonbonded pdb=" N ASN A 704 " pdb=" OD1 ASN A 704 " model vdw 2.568 3.120 nonbonded pdb=" C SER A 284 " pdb=" OG SER A 284 " model vdw 2.628 2.616 ... (remaining 56307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.002 0.031 7285 Z= 0.099 Angle : 0.583 11.327 9875 Z= 0.284 Chirality : 0.038 0.308 1148 Planarity : 0.003 0.035 1291 Dihedral : 19.087 89.550 2750 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.80 % Allowed : 33.42 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.29), residues: 915 helix: 1.04 (0.20), residues: 697 sheet: None (None), residues: 0 loop : 0.34 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 16 TYR 0.011 0.001 TYR A 248 PHE 0.004 0.001 PHE A 204 TRP 0.008 0.001 TRP A 864 HIS 0.001 0.000 HIS A 567 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 7285) covalent geometry : angle 0.58304 ( 9875) hydrogen bonds : bond 0.23337 ( 481) hydrogen bonds : angle 6.18902 ( 1419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9636 (mm110) cc_final: 0.9238 (tp-100) REVERT: A 104 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.6416 (m-10) REVERT: A 281 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7783 (mt-10) REVERT: A 288 ASP cc_start: 0.8476 (t0) cc_final: 0.8105 (t0) REVERT: A 291 MET cc_start: 0.8368 (mtp) cc_final: 0.8148 (mtm) REVERT: A 357 THR cc_start: 0.8909 (p) cc_final: 0.8697 (p) REVERT: A 395 GLU cc_start: 0.8187 (tp30) cc_final: 0.7781 (tp30) REVERT: A 413 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8774 (mm) REVERT: A 507 VAL cc_start: 0.9450 (OUTLIER) cc_final: 0.9236 (t) REVERT: A 533 MET cc_start: 0.7393 (mtp) cc_final: 0.7006 (mtp) REVERT: A 632 VAL cc_start: 0.9356 (t) cc_final: 0.9148 (m) REVERT: A 647 MET cc_start: 0.8068 (mmt) cc_final: 0.7667 (mmm) REVERT: A 834 LEU cc_start: 0.9374 (tp) cc_final: 0.9067 (pp) REVERT: B 32 ILE cc_start: 0.8151 (mm) cc_final: 0.7942 (mm) outliers start: 30 outliers final: 6 residues processed: 180 average time/residue: 0.0643 time to fit residues: 15.9852 Evaluate side-chains 101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 171 ASN A 208 ASN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.067330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048093 restraints weight = 29814.929| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.60 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7285 Z= 0.182 Angle : 0.687 9.518 9875 Z= 0.348 Chirality : 0.046 0.338 1148 Planarity : 0.005 0.065 1291 Dihedral : 4.784 48.978 996 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.96 % Allowed : 30.00 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.29), residues: 915 helix: 1.30 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.09 (0.50), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 679 TYR 0.009 0.002 TYR A 248 PHE 0.014 0.002 PHE A 370 TRP 0.014 0.002 TRP A 864 HIS 0.002 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7285) covalent geometry : angle 0.68717 ( 9875) hydrogen bonds : bond 0.04944 ( 481) hydrogen bonds : angle 4.16673 ( 1419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 105 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9721 (mm110) cc_final: 0.9405 (tp40) REVERT: A 104 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6540 (m-10) REVERT: A 281 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7922 (mt-10) REVERT: A 288 ASP cc_start: 0.8809 (t0) cc_final: 0.8534 (t0) REVERT: A 395 GLU cc_start: 0.8603 (tp30) cc_final: 0.8299 (tp30) REVERT: A 417 MET cc_start: 0.8649 (mpp) cc_final: 0.7959 (mpp) REVERT: A 624 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7420 (m) REVERT: A 647 MET cc_start: 0.8264 (mmt) cc_final: 0.7984 (mmm) REVERT: A 707 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6784 (ptt180) REVERT: B 49 LYS cc_start: 0.9127 (pttp) cc_final: 0.8925 (pptt) outliers start: 55 outliers final: 24 residues processed: 151 average time/residue: 0.0602 time to fit residues: 12.7504 Evaluate side-chains 116 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 0.0470 chunk 52 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.067259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048211 restraints weight = 29423.827| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.55 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7285 Z= 0.143 Angle : 0.606 7.533 9875 Z= 0.305 Chirality : 0.042 0.250 1148 Planarity : 0.004 0.038 1291 Dihedral : 4.280 35.932 991 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.81 % Allowed : 30.25 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.30), residues: 915 helix: 1.43 (0.21), residues: 705 sheet: None (None), residues: 0 loop : 0.11 (0.48), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 613 TYR 0.009 0.001 TYR A 661 PHE 0.029 0.001 PHE A 24 TRP 0.016 0.001 TRP A 864 HIS 0.002 0.000 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7285) covalent geometry : angle 0.60573 ( 9875) hydrogen bonds : bond 0.04670 ( 481) hydrogen bonds : angle 3.93706 ( 1419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9727 (mm110) cc_final: 0.9399 (tp-100) REVERT: A 104 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.6496 (m-10) REVERT: A 164 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8697 (mp0) REVERT: A 281 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 288 ASP cc_start: 0.8865 (t0) cc_final: 0.8633 (t0) REVERT: A 395 GLU cc_start: 0.8697 (tp30) cc_final: 0.8431 (tp30) REVERT: A 417 MET cc_start: 0.8778 (mpp) cc_final: 0.8111 (mpp) REVERT: A 627 ASP cc_start: 0.8903 (m-30) cc_final: 0.8564 (m-30) REVERT: A 707 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6806 (ptt180) outliers start: 38 outliers final: 23 residues processed: 134 average time/residue: 0.0649 time to fit residues: 12.0978 Evaluate side-chains 114 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 68 optimal weight: 0.0020 chunk 3 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 59 optimal weight: 0.0770 chunk 12 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.068315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049019 restraints weight = 29816.899| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.65 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7285 Z= 0.121 Angle : 0.589 8.001 9875 Z= 0.291 Chirality : 0.041 0.246 1148 Planarity : 0.004 0.038 1291 Dihedral : 4.100 36.797 989 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.92 % Allowed : 31.52 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.30), residues: 915 helix: 1.44 (0.21), residues: 708 sheet: None (None), residues: 0 loop : 0.04 (0.48), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 28 TYR 0.006 0.001 TYR A 661 PHE 0.020 0.001 PHE A 24 TRP 0.020 0.001 TRP A 864 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7285) covalent geometry : angle 0.58863 ( 9875) hydrogen bonds : bond 0.04044 ( 481) hydrogen bonds : angle 3.75379 ( 1419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9724 (mm110) cc_final: 0.9411 (tp-100) REVERT: A 104 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6620 (m-10) REVERT: A 164 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8684 (mp0) REVERT: A 281 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 288 ASP cc_start: 0.8843 (t0) cc_final: 0.8624 (t0) REVERT: A 395 GLU cc_start: 0.8706 (tp30) cc_final: 0.8459 (tp30) REVERT: A 417 MET cc_start: 0.8733 (mpp) cc_final: 0.8094 (mpp) REVERT: A 449 LEU cc_start: 0.8770 (mt) cc_final: 0.8551 (mt) REVERT: A 568 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8178 (mp) REVERT: A 627 ASP cc_start: 0.8892 (m-30) cc_final: 0.8553 (m-30) REVERT: A 707 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6763 (ptt180) REVERT: B 49 LYS cc_start: 0.9025 (pptt) cc_final: 0.8754 (pptt) outliers start: 31 outliers final: 17 residues processed: 130 average time/residue: 0.0599 time to fit residues: 11.1565 Evaluate side-chains 113 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 454 GLN A 759 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.066806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.047184 restraints weight = 29750.016| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.60 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7285 Z= 0.163 Angle : 0.601 8.684 9875 Z= 0.306 Chirality : 0.042 0.214 1148 Planarity : 0.004 0.038 1291 Dihedral : 4.146 35.680 989 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.94 % Allowed : 30.76 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.29), residues: 915 helix: 1.45 (0.21), residues: 705 sheet: None (None), residues: 0 loop : 0.09 (0.48), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 28 TYR 0.024 0.002 TYR A 769 PHE 0.014 0.002 PHE A 24 TRP 0.020 0.002 TRP A 864 HIS 0.003 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7285) covalent geometry : angle 0.60056 ( 9875) hydrogen bonds : bond 0.04089 ( 481) hydrogen bonds : angle 3.85314 ( 1419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9739 (mm110) cc_final: 0.9450 (tp-100) REVERT: A 104 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6780 (m-10) REVERT: A 164 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8798 (mp0) REVERT: A 281 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 410 MET cc_start: 0.9500 (mmm) cc_final: 0.9285 (mmm) REVERT: A 417 MET cc_start: 0.8790 (mpp) cc_final: 0.8188 (mpp) REVERT: A 568 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 627 ASP cc_start: 0.9019 (m-30) cc_final: 0.8616 (m-30) REVERT: A 707 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6781 (ptt180) REVERT: A 788 MET cc_start: 0.9503 (mpp) cc_final: 0.9082 (mpp) REVERT: B 49 LYS cc_start: 0.9018 (pptt) cc_final: 0.8794 (pptt) outliers start: 39 outliers final: 23 residues processed: 133 average time/residue: 0.0612 time to fit residues: 11.2141 Evaluate side-chains 116 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 HIS ** 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 = 0.3521 r_free = 0.3521 target = 0.067052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.047585 restraints weight = 29608.065| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.62 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7285 Z= 0.130 Angle : 0.596 7.689 9875 Z= 0.300 Chirality : 0.041 0.228 1148 Planarity : 0.004 0.037 1291 Dihedral : 4.134 37.023 989 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.92 % Allowed : 32.28 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.30), residues: 915 helix: 1.50 (0.21), residues: 707 sheet: None (None), residues: 0 loop : -0.01 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 613 TYR 0.009 0.001 TYR A 661 PHE 0.012 0.001 PHE A 24 TRP 0.013 0.001 TRP A 864 HIS 0.003 0.000 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7285) covalent geometry : angle 0.59628 ( 9875) hydrogen bonds : bond 0.03738 ( 481) hydrogen bonds : angle 3.75098 ( 1419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9745 (mm110) cc_final: 0.9466 (tp-100) REVERT: A 104 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: A 164 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8859 (mp0) REVERT: A 281 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 388 MET cc_start: 0.8741 (tpp) cc_final: 0.8304 (tpp) REVERT: A 417 MET cc_start: 0.8796 (mpp) cc_final: 0.8203 (mpp) REVERT: A 530 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 568 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 627 ASP cc_start: 0.9013 (m-30) cc_final: 0.8667 (m-30) REVERT: A 707 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6928 (ptt180) REVERT: A 788 MET cc_start: 0.9511 (mpp) cc_final: 0.9071 (mpp) REVERT: B 49 LYS cc_start: 0.8993 (pptt) cc_final: 0.8749 (pptt) outliers start: 31 outliers final: 23 residues processed: 121 average time/residue: 0.0627 time to fit residues: 10.7380 Evaluate side-chains 115 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 HIS ** 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 = 0.3532 r_free = 0.3532 target = 0.067545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048096 restraints weight = 29766.680| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.65 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7285 Z= 0.122 Angle : 0.606 9.158 9875 Z= 0.301 Chirality : 0.041 0.296 1148 Planarity : 0.004 0.052 1291 Dihedral : 4.051 37.775 989 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.92 % Allowed : 32.78 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.30), residues: 915 helix: 1.61 (0.21), residues: 702 sheet: None (None), residues: 0 loop : 0.15 (0.47), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 613 TYR 0.008 0.001 TYR A 249 PHE 0.011 0.001 PHE A 24 TRP 0.021 0.001 TRP A 864 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7285) covalent geometry : angle 0.60596 ( 9875) hydrogen bonds : bond 0.03468 ( 481) hydrogen bonds : angle 3.67837 ( 1419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9742 (mm110) cc_final: 0.9494 (tp-100) REVERT: A 164 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8873 (mp0) REVERT: A 255 TYR cc_start: 0.7674 (t80) cc_final: 0.7473 (t80) REVERT: A 388 MET cc_start: 0.8725 (tpp) cc_final: 0.8296 (tpp) REVERT: A 417 MET cc_start: 0.8731 (mpp) cc_final: 0.8368 (mpp) REVERT: A 568 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 612 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9359 (pp) REVERT: A 627 ASP cc_start: 0.9008 (m-30) cc_final: 0.8643 (m-30) REVERT: A 707 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6944 (ptt180) REVERT: A 740 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9164 (tt0) REVERT: A 788 MET cc_start: 0.9527 (mpp) cc_final: 0.9121 (mpp) REVERT: B 33 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: B 49 LYS cc_start: 0.9016 (pptt) cc_final: 0.8762 (pptt) outliers start: 31 outliers final: 21 residues processed: 122 average time/residue: 0.0633 time to fit residues: 11.0265 Evaluate side-chains 120 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain B residue 33 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 HIS ** 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 = 0.3532 r_free = 0.3532 target = 0.067489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048100 restraints weight = 29900.402| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.69 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7285 Z= 0.122 Angle : 0.610 8.508 9875 Z= 0.304 Chirality : 0.040 0.260 1148 Planarity : 0.004 0.049 1291 Dihedral : 3.783 18.652 985 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.80 % Allowed : 32.78 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.30), residues: 915 helix: 1.56 (0.21), residues: 704 sheet: None (None), residues: 0 loop : 0.19 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 613 TYR 0.008 0.001 TYR A 249 PHE 0.010 0.001 PHE A 24 TRP 0.013 0.001 TRP A 864 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7285) covalent geometry : angle 0.60994 ( 9875) hydrogen bonds : bond 0.03512 ( 481) hydrogen bonds : angle 3.69493 ( 1419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9744 (mm110) cc_final: 0.9500 (tp-100) REVERT: A 164 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8886 (mp0) REVERT: A 281 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8089 (mt-10) REVERT: A 388 MET cc_start: 0.8729 (tpp) cc_final: 0.8292 (tpp) REVERT: A 417 MET cc_start: 0.8727 (mpp) cc_final: 0.8340 (mpp) REVERT: A 437 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7917 (mm-30) REVERT: A 449 LEU cc_start: 0.8911 (mt) cc_final: 0.8542 (mt) REVERT: A 568 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 627 ASP cc_start: 0.9037 (m-30) cc_final: 0.8663 (m-30) REVERT: A 707 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6948 (ptt180) REVERT: A 767 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8819 (mm-30) REVERT: A 788 MET cc_start: 0.9523 (mpp) cc_final: 0.9116 (mpp) REVERT: B 46 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8820 (tm-30) REVERT: B 49 LYS cc_start: 0.9028 (pptt) cc_final: 0.8720 (pptt) outliers start: 30 outliers final: 26 residues processed: 119 average time/residue: 0.0644 time to fit residues: 10.8873 Evaluate side-chains 119 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain B residue 44 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.067493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048067 restraints weight = 29588.707| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.62 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7285 Z= 0.123 Angle : 0.617 9.605 9875 Z= 0.305 Chirality : 0.040 0.254 1148 Planarity : 0.004 0.040 1291 Dihedral : 3.762 17.990 985 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.05 % Allowed : 32.78 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.30), residues: 915 helix: 1.63 (0.21), residues: 702 sheet: None (None), residues: 0 loop : 0.21 (0.47), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 27 TYR 0.021 0.001 TYR A 255 PHE 0.014 0.001 PHE A 24 TRP 0.031 0.001 TRP A 864 HIS 0.001 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7285) covalent geometry : angle 0.61739 ( 9875) hydrogen bonds : bond 0.03415 ( 481) hydrogen bonds : angle 3.72128 ( 1419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9757 (mm110) cc_final: 0.9516 (tp-100) REVERT: A 164 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8899 (mp0) REVERT: A 179 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8531 (mm-40) REVERT: A 388 MET cc_start: 0.8729 (tpp) cc_final: 0.8284 (tpp) REVERT: A 417 MET cc_start: 0.8693 (mpp) cc_final: 0.8301 (mpp) REVERT: A 449 LEU cc_start: 0.8918 (mt) cc_final: 0.8534 (mt) REVERT: A 568 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 627 ASP cc_start: 0.9050 (m-30) cc_final: 0.8651 (m-30) REVERT: A 707 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6889 (ptt180) REVERT: A 740 GLN cc_start: 0.9574 (OUTLIER) cc_final: 0.9169 (tt0) REVERT: A 788 MET cc_start: 0.9518 (mpp) cc_final: 0.9123 (mpp) REVERT: B 27 MET cc_start: 0.9165 (mmp) cc_final: 0.8948 (mmm) REVERT: B 44 ASP cc_start: 0.9379 (t0) cc_final: 0.9040 (m-30) REVERT: B 46 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8829 (tm-30) REVERT: B 49 LYS cc_start: 0.9047 (pptt) cc_final: 0.8731 (pptt) outliers start: 32 outliers final: 25 residues processed: 118 average time/residue: 0.0659 time to fit residues: 10.9618 Evaluate side-chains 119 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 40 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 HIS ** 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 = 0.3530 r_free = 0.3530 target = 0.067419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.048116 restraints weight = 29820.931| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.66 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7285 Z= 0.123 Angle : 0.627 9.407 9875 Z= 0.310 Chirality : 0.040 0.249 1148 Planarity : 0.004 0.041 1291 Dihedral : 3.759 18.182 985 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.92 % Allowed : 33.04 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.30), residues: 915 helix: 1.63 (0.21), residues: 700 sheet: None (None), residues: 0 loop : 0.17 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 27 TYR 0.012 0.001 TYR A 255 PHE 0.013 0.001 PHE A 474 TRP 0.013 0.001 TRP A 864 HIS 0.001 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7285) covalent geometry : angle 0.62698 ( 9875) hydrogen bonds : bond 0.03459 ( 481) hydrogen bonds : angle 3.70096 ( 1419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9753 (mm110) cc_final: 0.9518 (tp-100) REVERT: A 164 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8891 (mp0) REVERT: A 388 MET cc_start: 0.8721 (tpp) cc_final: 0.8271 (tpp) REVERT: A 417 MET cc_start: 0.8663 (mpp) cc_final: 0.8265 (mpp) REVERT: A 449 LEU cc_start: 0.8913 (mt) cc_final: 0.8525 (mt) REVERT: A 474 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8854 (t80) REVERT: A 627 ASP cc_start: 0.9071 (m-30) cc_final: 0.8649 (m-30) REVERT: A 740 GLN cc_start: 0.9585 (OUTLIER) cc_final: 0.9183 (tt0) REVERT: A 767 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8778 (mm-30) REVERT: A 788 MET cc_start: 0.9515 (mpp) cc_final: 0.9145 (mpp) REVERT: B 27 MET cc_start: 0.9167 (mmp) cc_final: 0.8940 (mmm) REVERT: B 44 ASP cc_start: 0.9352 (OUTLIER) cc_final: 0.9035 (m-30) REVERT: B 46 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8851 (tm-30) REVERT: B 49 LYS cc_start: 0.9061 (pptt) cc_final: 0.8754 (pptt) outliers start: 31 outliers final: 24 residues processed: 116 average time/residue: 0.0703 time to fit residues: 11.1964 Evaluate side-chains 114 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 HIS ** 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 = 0.3526 r_free = 0.3526 target = 0.067302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047989 restraints weight = 29721.684| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.65 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7285 Z= 0.125 Angle : 0.637 9.728 9875 Z= 0.314 Chirality : 0.041 0.246 1148 Planarity : 0.004 0.039 1291 Dihedral : 3.761 17.827 985 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.80 % Allowed : 32.91 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.30), residues: 915 helix: 1.62 (0.21), residues: 700 sheet: None (None), residues: 0 loop : 0.21 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 27 TYR 0.011 0.001 TYR A 249 PHE 0.011 0.001 PHE A 24 TRP 0.041 0.002 TRP A 864 HIS 0.001 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7285) covalent geometry : angle 0.63669 ( 9875) hydrogen bonds : bond 0.03391 ( 481) hydrogen bonds : angle 3.73369 ( 1419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.97 seconds wall clock time: 24 minutes 28.23 seconds (1468.23 seconds total)