Starting phenix.real_space_refine on Sun Sep 13 21:36:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mir_23862/09_2026/7mir_23862_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mir_23862/09_2026/7mir_23862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mir_23862/09_2026/7mir_23862_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mir_23862/09_2026/7mir_23862_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mir_23862/09_2026/7mir_23862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mir_23862/09_2026/7mir_23862.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 Mg 2 5.21 5 S 45 5.16 5 C 8207 2.51 5 N 2231 2.21 5 O 2507 1.98 5 H 12748 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25745 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 12193 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 31, 'TRANS': 718} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 3 Chain: "C" Number of atoms: 11500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 11500 Classifications: {'peptide': 724} Link IDs: {'PTRANS': 27, 'TRANS': 696} Chain breaks: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'AMP%rna2p': 1, 'ATP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.15 Number of scatterers: 25745 At special positions: 0 Unit cell: (137.16, 123.12, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 S 45 16.00 P 4 15.00 Mg 2 11.99 O 2507 8.00 N 2231 7.00 C 8207 6.00 H 12748 1.00 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 Atom "ATOM 5826 OH TYR A 452 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 750.0 milliseconds 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3044 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 12 sheets defined 61.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 135 through 158 removed outlier: 3.611A pdb=" N THR A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 182 Processing helix chain 'A' and resid 184 through 206 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.088A pdb=" N HIS A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.768A pdb=" N PHE A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.677A pdb=" N LEU A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 306 " --> pdb=" O HIS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 374 through 396 removed outlier: 4.151A pdb=" N LEU A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.738A pdb=" N THR A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 459 through 480 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.869A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 593 through 622 removed outlier: 3.648A pdb=" N TYR A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 627 through 655 Processing helix chain 'A' and resid 657 through 669 removed outlier: 3.678A pdb=" N ARG A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 683 through 689 removed outlier: 4.145A pdb=" N TYR A 686 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 689 " --> pdb=" O TYR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 702 removed outlier: 3.785A pdb=" N SER A 700 " --> pdb=" O MET A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 774 removed outlier: 3.555A pdb=" N GLN A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 794 Processing helix chain 'A' and resid 800 through 817 Processing helix chain 'A' and resid 826 through 848 Processing helix chain 'B' and resid 6 through 21 Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 66 through 78 Processing helix chain 'B' and resid 83 through 93 removed outlier: 4.070A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.715A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'C' and resid 237 through 251 removed outlier: 3.674A pdb=" N LYS C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 302 Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 343 through 365 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 376 through 389 Processing helix chain 'C' and resid 397 through 410 Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 417 through 431 removed outlier: 3.794A pdb=" N PHE C 421 " --> pdb=" O PRO C 417 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG C 431 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 452 removed outlier: 3.789A pdb=" N ARG C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 447 " --> pdb=" O GLY C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 521 Processing helix chain 'C' and resid 522 through 527 Processing helix chain 'C' and resid 544 through 553 Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.721A pdb=" N ALA C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 586 Proline residue: C 582 - end of helix Processing helix chain 'C' and resid 599 through 615 removed outlier: 3.622A pdb=" N ALA C 604 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 643 removed outlier: 3.575A pdb=" N PHE C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 651 Processing helix chain 'C' and resid 653 through 668 removed outlier: 3.825A pdb=" N ILE C 657 " --> pdb=" O ASN C 653 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP C 661 " --> pdb=" O ILE C 657 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR C 662 " --> pdb=" O GLY C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 696 Processing helix chain 'C' and resid 700 through 714 Processing helix chain 'C' and resid 715 through 727 removed outlier: 4.365A pdb=" N ARG C 721 " --> pdb=" O TRP C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 756 Proline residue: C 746 - end of helix Processing helix chain 'C' and resid 771 through 788 removed outlier: 3.842A pdb=" N ASN C 788 " --> pdb=" O ALA C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 809 Processing helix chain 'C' and resid 810 through 814 removed outlier: 3.709A pdb=" N MET C 813 " --> pdb=" O LEU C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 832 removed outlier: 3.774A pdb=" N VAL C 828 " --> pdb=" O GLU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 904 Processing helix chain 'C' and resid 912 through 932 removed outlier: 3.800A pdb=" N PHE C 916 " --> pdb=" O ALA C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1075 removed outlier: 3.916A pdb=" N ALA C1075 " --> pdb=" O GLN C1071 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1086 Processing helix chain 'C' and resid 1100 through 1118 Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 293 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.886A pdb=" N LEU A 346 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER A 357 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 406 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS A 444 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 482 through 483 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA7, first strand: chain 'C' and resid 265 through 267 Processing sheet with id=AA8, first strand: chain 'C' and resid 459 through 460 Processing sheet with id=AA9, first strand: chain 'C' and resid 619 through 620 removed outlier: 4.114A pdb=" N HIS C 623 " --> pdb=" O HIS C 620 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 670 through 671 removed outlier: 3.655A pdb=" N VAL C 682 " --> pdb=" O GLU C 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 763 through 768 removed outlier: 6.940A pdb=" N ARG C 890 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU C 880 " --> pdb=" O ARG C 890 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 892 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL C 878 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C 894 " --> pdb=" O VAL C 876 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 819 through 822 712 hydrogen bonds defined for protein. 2040 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: 6.20 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12741 1.03 - 1.23: 8 1.23 - 1.42: 5591 1.42 - 1.61: 7583 1.61 - 1.81: 83 Bond restraints: 26006 Sorted by residual: bond pdb=" ND2 ASN A 733 " pdb="HD22 ASN A 733 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN A 733 " pdb="HD21 ASN A 733 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C4 AMP A 901 " pdb=" C5 AMP A 901 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C5 AMP A 901 " pdb=" C6 AMP A 901 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O5' ATP A 904 " pdb=" PA ATP A 904 " ideal model delta sigma weight residual 1.579 1.612 -0.033 1.10e-02 8.26e+03 8.77e+00 ... (remaining 26001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 46837 2.46 - 4.91: 94 4.91 - 7.37: 5 7.37 - 9.82: 4 9.82 - 12.28: 1 Bond angle restraints: 46941 Sorted by residual: angle pdb=" PB ATP A 904 " pdb=" O3B ATP A 904 " pdb=" PG ATP A 904 " ideal model delta sigma weight residual 139.87 132.08 7.79 1.00e+00 1.00e+00 6.06e+01 angle pdb=" PA ATP A 904 " pdb=" O3A ATP A 904 " pdb=" PB ATP A 904 " ideal model delta sigma weight residual 136.83 131.99 4.84 1.00e+00 1.00e+00 2.34e+01 angle pdb=" O2P AMP A 901 " pdb=" P AMP A 901 " pdb=" O3P AMP A 901 " ideal model delta sigma weight residual 119.90 107.62 12.28 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C LEU C 369 " pdb=" N ILE C 370 " pdb=" CA ILE C 370 " ideal model delta sigma weight residual 120.24 122.54 -2.30 6.30e-01 2.52e+00 1.34e+01 angle pdb=" C ILE C 370 " pdb=" CA ILE C 370 " pdb=" CB ILE C 370 " ideal model delta sigma weight residual 114.35 110.56 3.79 1.06e+00 8.90e-01 1.28e+01 ... (remaining 46936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 11111 17.53 - 35.07: 845 35.07 - 52.60: 207 52.60 - 70.14: 55 70.14 - 87.67: 20 Dihedral angle restraints: 12238 sinusoidal: 6686 harmonic: 5552 Sorted by residual: dihedral pdb=" CA SER C 259 " pdb=" C SER C 259 " pdb=" N VAL C 260 " pdb=" CA VAL C 260 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG ARG C 890 " pdb=" CD ARG C 890 " pdb=" NE ARG C 890 " pdb=" CZ ARG C 890 " ideal model delta sinusoidal sigma weight residual -180.00 -135.39 -44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 660 " pdb=" CD ARG A 660 " pdb=" NE ARG A 660 " pdb=" CZ ARG A 660 " ideal model delta sinusoidal sigma weight residual -90.00 -134.58 44.58 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 12235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1667 0.050 - 0.100: 243 0.100 - 0.150: 46 0.150 - 0.200: 1 0.200 - 0.250: 1 Chirality restraints: 1958 Sorted by residual: chirality pdb=" CA ASN A 733 " pdb=" N ASN A 733 " pdb=" C ASN A 733 " pdb=" CB ASN A 733 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE A 656 " pdb=" N ILE A 656 " pdb=" C ILE A 656 " pdb=" CB ILE A 656 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE A 134 " pdb=" N ILE A 134 " pdb=" C ILE A 134 " pdb=" CB ILE A 134 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1955 not shown) Planarity restraints: 3853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 733 " 0.064 2.00e-02 2.50e+03 6.45e-02 6.24e+01 pdb=" CG ASN A 733 " 0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 733 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 733 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 733 " -0.091 2.00e-02 2.50e+03 pdb="HD22 ASN A 733 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AMP A 901 " -0.062 2.00e-02 2.50e+03 2.74e-02 2.07e+01 pdb=" C2 AMP A 901 " 0.010 2.00e-02 2.50e+03 pdb=" C4 AMP A 901 " 0.019 2.00e-02 2.50e+03 pdb=" C5 AMP A 901 " 0.017 2.00e-02 2.50e+03 pdb=" C6 AMP A 901 " -0.002 2.00e-02 2.50e+03 pdb=" C8 AMP A 901 " 0.019 2.00e-02 2.50e+03 pdb=" N1 AMP A 901 " -0.003 2.00e-02 2.50e+03 pdb=" N3 AMP A 901 " 0.019 2.00e-02 2.50e+03 pdb=" N6 AMP A 901 " -0.048 2.00e-02 2.50e+03 pdb=" N7 AMP A 901 " 0.023 2.00e-02 2.50e+03 pdb=" N9 AMP A 901 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 680 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO C 681 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 681 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 681 " 0.021 5.00e-02 4.00e+02 ... (remaining 3850 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1112 2.19 - 2.79: 51992 2.79 - 3.39: 71497 3.39 - 4.00: 93852 4.00 - 4.60: 145364 Nonbonded interactions: 363817 Sorted by model distance: nonbonded pdb=" HD1 HIS C 281 " pdb=" OD2 ASP C 410 " model vdw 1.585 2.450 nonbonded pdb="HH22 ARG A 660 " pdb=" OE2 GLU B 15 " model vdw 1.595 2.450 nonbonded pdb=" HE2 HIS A 492 " pdb=" O3P AMP A 901 " model vdw 1.606 2.450 nonbonded pdb=" OE2 GLU C 352 " pdb="HH22 ARG C 355 " model vdw 1.613 2.450 nonbonded pdb=" H GLU A 221 " pdb=" OD2 ASP A 793 " model vdw 1.616 2.450 ... (remaining 363812 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: 5.180 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: 0.170 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 0.106 13258 Z= 0.142 Angle : 0.485 12.277 17903 Z= 0.261 Chirality : 0.037 0.250 1958 Planarity : 0.003 0.045 2320 Dihedral : 14.430 87.670 5023 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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 (0.22), residues: 1583 helix: 2.22 (0.18), residues: 868 sheet: 0.71 (0.52), residues: 94 loop : -0.13 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.009 0.001 TYR C 383 PHE 0.019 0.001 PHE C 719 TRP 0.010 0.001 TRP A 845 HIS 0.011 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (13258) covalent geometry : angle 0.48465 / 0.26 (17903) hydrogen bonds : bond 0.11935 / 7.71 ( 712) hydrogen bonds : angle 5.17645 / 3.80 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 1.3110 time to fit residues: 238.9165 Evaluate side-chains 122 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 695 GLN A 726 HIS B 50 GLN C 537 GLN C 611 GLN C 696 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091578 restraints weight = 50841.178| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.77 r_work: 0.3042 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13258 Z= 0.181 Angle : 0.522 7.926 17903 Z= 0.281 Chirality : 0.038 0.142 1958 Planarity : 0.004 0.042 2320 Dihedral : 5.838 86.076 1782 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.49 % Allowed : 6.97 % Favored : 92.54 % 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: 1.59 (0.21), residues: 1583 helix: 2.03 (0.17), residues: 883 sheet: 0.48 (0.51), residues: 94 loop : -0.30 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 127 TYR 0.014 0.002 TYR C 383 PHE 0.024 0.002 PHE C 719 TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS C 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (13258) covalent geometry : angle 0.52241 / 0.28 (17903) hydrogen bonds : bond 0.05612 / 3.70 ( 712) hydrogen bonds : angle 4.43153 / 3.20 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7819 (ttm170) outliers start: 7 outliers final: 5 residues processed: 141 average time/residue: 1.1877 time to fit residues: 184.4712 Evaluate side-chains 131 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 600 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 4 GLN B 50 GLN C 537 GLN C 611 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090829 restraints weight = 51037.751| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.76 r_work: 0.3030 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13258 Z= 0.194 Angle : 0.526 8.108 17903 Z= 0.284 Chirality : 0.039 0.147 1958 Planarity : 0.004 0.047 2320 Dihedral : 5.693 83.172 1782 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.06 % Allowed : 8.37 % Favored : 90.57 % 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: 1.45 (0.21), residues: 1583 helix: 1.93 (0.17), residues: 884 sheet: 0.35 (0.50), residues: 94 loop : -0.37 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.015 0.002 TYR C 383 PHE 0.023 0.002 PHE C 719 TRP 0.008 0.002 TRP A 277 HIS 0.004 0.001 HIS C 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (13258) covalent geometry : angle 0.52596 / 0.28 (17903) hydrogen bonds : bond 0.05778 / 3.81 ( 712) hydrogen bonds : angle 4.37201 / 3.16 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7777 (ttm170) REVERT: A 767 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: B 7 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: B 72 MET cc_start: 0.6624 (mtp) cc_final: 0.6174 (mtp) REVERT: B 78 LYS cc_start: 0.7111 (tppt) cc_final: 0.6853 (mptt) outliers start: 15 outliers final: 6 residues processed: 139 average time/residue: 1.3451 time to fit residues: 204.3324 Evaluate side-chains 131 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 79 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 0.0040 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 50 GLN C 537 GLN C 611 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095218 restraints weight = 52467.859| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.72 r_work: 0.3102 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13258 Z= 0.151 Angle : 0.497 7.715 17903 Z= 0.266 Chirality : 0.037 0.153 1958 Planarity : 0.004 0.043 2320 Dihedral : 5.524 80.485 1782 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.84 % Allowed : 9.43 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1583 helix: 2.03 (0.17), residues: 891 sheet: 0.22 (0.49), residues: 99 loop : -0.38 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.012 0.002 TYR C 383 PHE 0.023 0.001 PHE C 719 TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (13258) covalent geometry : angle 0.49729 / 0.27 (17903) hydrogen bonds : bond 0.05150 / 3.39 ( 712) hydrogen bonds : angle 4.24081 / 3.06 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7787 (ttm170) REVERT: A 767 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: A 773 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7970 (mp) REVERT: B 78 LYS cc_start: 0.7118 (tppt) cc_final: 0.6850 (mptt) REVERT: C 310 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7398 (mtmm) REVERT: C 645 MET cc_start: 0.8572 (mmm) cc_final: 0.8274 (mmm) outliers start: 12 outliers final: 5 residues processed: 135 average time/residue: 1.4043 time to fit residues: 207.8569 Evaluate side-chains 129 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 82 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 chunk 149 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 50 GLN C 537 GLN ** C 696 ASN ** 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 = 0.3677 r_free = 0.3677 target = 0.126400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095124 restraints weight = 52502.405| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.74 r_work: 0.3086 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13258 Z= 0.152 Angle : 0.495 7.683 17903 Z= 0.265 Chirality : 0.037 0.145 1958 Planarity : 0.004 0.041 2320 Dihedral : 5.480 80.230 1782 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.99 % Allowed : 10.27 % Favored : 88.74 % 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: 1.57 (0.21), residues: 1583 helix: 2.08 (0.17), residues: 884 sheet: 0.20 (0.49), residues: 99 loop : -0.37 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.012 0.002 TYR C 383 PHE 0.023 0.002 PHE C 719 TRP 0.007 0.001 TRP A 277 HIS 0.006 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (13258) covalent geometry : angle 0.49530 / 0.27 (17903) hydrogen bonds : bond 0.05135 / 3.38 ( 712) hydrogen bonds : angle 4.19039 / 3.02 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7802 (ttm170) REVERT: A 767 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: A 773 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8003 (mp) REVERT: B 78 LYS cc_start: 0.7112 (tppt) cc_final: 0.6907 (mptt) REVERT: C 310 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7416 (mtmt) REVERT: C 645 MET cc_start: 0.8533 (mmm) cc_final: 0.8273 (mmm) REVERT: C 920 GLN cc_start: 0.7446 (mp10) cc_final: 0.6869 (mp10) outliers start: 14 outliers final: 7 residues processed: 136 average time/residue: 1.4299 time to fit residues: 212.8620 Evaluate side-chains 130 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 930 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 50 GLN C 537 GLN C 611 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091806 restraints weight = 50969.322| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.85 r_work: 0.3024 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13258 Z= 0.210 Angle : 0.542 8.119 17903 Z= 0.293 Chirality : 0.039 0.148 1958 Planarity : 0.004 0.050 2320 Dihedral : 5.671 82.717 1782 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.13 % Allowed : 10.34 % Favored : 88.53 % 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: 1.38 (0.21), residues: 1583 helix: 1.89 (0.17), residues: 884 sheet: 0.27 (0.50), residues: 94 loop : -0.41 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.014 0.002 TYR C 383 PHE 0.022 0.002 PHE C 719 TRP 0.009 0.002 TRP A 277 HIS 0.007 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (13258) covalent geometry : angle 0.54173 / 0.29 (17903) hydrogen bonds : bond 0.05889 / 3.90 ( 712) hydrogen bonds : angle 4.32395 / 3.12 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7690 (ttm170) REVERT: A 773 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 7 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: B 78 LYS cc_start: 0.7091 (tppt) cc_final: 0.6764 (mptt) REVERT: C 310 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7469 (mtmt) REVERT: C 645 MET cc_start: 0.8475 (mmm) cc_final: 0.8196 (mmm) REVERT: C 870 ASP cc_start: 0.7345 (t70) cc_final: 0.6968 (t70) REVERT: C 920 GLN cc_start: 0.7467 (mp10) cc_final: 0.6866 (mp10) REVERT: C 1111 LYS cc_start: 0.7840 (tmtm) cc_final: 0.7372 (tmmt) REVERT: C 1114 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6234 (tp30) outliers start: 16 outliers final: 8 residues processed: 137 average time/residue: 1.3467 time to fit residues: 201.6000 Evaluate side-chains 127 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 50 GLN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095790 restraints weight = 52574.412| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.73 r_work: 0.3106 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13258 Z= 0.126 Angle : 0.485 7.575 17903 Z= 0.258 Chirality : 0.036 0.145 1958 Planarity : 0.004 0.046 2320 Dihedral : 5.428 79.137 1782 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.20 % Allowed : 10.56 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1583 helix: 2.17 (0.17), residues: 883 sheet: 0.37 (0.51), residues: 92 loop : -0.33 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.011 0.001 TYR C 383 PHE 0.023 0.001 PHE C 719 TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13258) covalent geometry : angle 0.48532 / 0.26 (17903) hydrogen bonds : bond 0.04747 / 3.12 ( 712) hydrogen bonds : angle 4.13136 / 2.97 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7792 (ttm170) REVERT: A 767 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: A 773 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8001 (mp) REVERT: B 78 LYS cc_start: 0.7160 (tppt) cc_final: 0.6956 (tptt) REVERT: C 310 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7394 (mtmm) REVERT: C 645 MET cc_start: 0.8440 (mmm) cc_final: 0.8096 (mmm) REVERT: C 920 GLN cc_start: 0.7562 (mp10) cc_final: 0.6958 (mp10) REVERT: C 1111 LYS cc_start: 0.7804 (tmtm) cc_final: 0.7319 (tmmt) outliers start: 17 outliers final: 6 residues processed: 135 average time/residue: 1.3520 time to fit residues: 199.9124 Evaluate side-chains 128 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 930 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 157 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 50 GLN C 537 GLN C 696 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.091060 restraints weight = 50919.868| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.81 r_work: 0.3012 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13258 Z= 0.258 Angle : 0.580 8.745 17903 Z= 0.315 Chirality : 0.041 0.152 1958 Planarity : 0.004 0.047 2320 Dihedral : 5.807 84.217 1782 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.06 % Allowed : 10.84 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1583 helix: 1.75 (0.17), residues: 885 sheet: 0.36 (0.49), residues: 99 loop : -0.43 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 854 TYR 0.016 0.002 TYR C 383 PHE 0.025 0.002 PHE A 475 TRP 0.009 0.002 TRP A 277 HIS 0.007 0.002 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.26 (13258) covalent geometry : angle 0.58044 / 0.32 (17903) hydrogen bonds : bond 0.06398 / 4.24 ( 712) hydrogen bonds : angle 4.40683 / 3.18 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7713 (ttm170) REVERT: A 773 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8052 (mp) REVERT: B 72 MET cc_start: 0.6539 (mtp) cc_final: 0.6331 (mtp) REVERT: B 78 LYS cc_start: 0.7055 (tppt) cc_final: 0.6756 (mptt) REVERT: C 310 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7565 (mtmm) REVERT: C 416 GLN cc_start: 0.7408 (tp40) cc_final: 0.7099 (tp40) REVERT: C 645 MET cc_start: 0.8470 (mmm) cc_final: 0.8187 (mmm) REVERT: C 920 GLN cc_start: 0.7529 (mp10) cc_final: 0.6969 (mp10) REVERT: C 1111 LYS cc_start: 0.7810 (tmtm) cc_final: 0.7351 (tmmt) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 1.3585 time to fit residues: 191.6428 Evaluate side-chains 123 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 930 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 96 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 50 GLN C 537 GLN C 696 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094191 restraints weight = 50660.937| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.80 r_work: 0.3063 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13258 Z= 0.117 Angle : 0.488 8.292 17903 Z= 0.259 Chirality : 0.036 0.143 1958 Planarity : 0.004 0.044 2320 Dihedral : 5.447 79.350 1782 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.91 % Allowed : 11.19 % Favored : 87.90 % 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: 1.64 (0.21), residues: 1583 helix: 2.12 (0.17), residues: 883 sheet: 0.36 (0.51), residues: 92 loop : -0.33 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.011 0.001 TYR C 383 PHE 0.024 0.001 PHE C 719 TRP 0.007 0.001 TRP C 717 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (13258) covalent geometry : angle 0.48818 / 0.26 (17903) hydrogen bonds : bond 0.04678 / 3.08 ( 712) hydrogen bonds : angle 4.14548 / 2.98 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8005 (mp) REVERT: B 72 MET cc_start: 0.6593 (mtp) cc_final: 0.6342 (mtp) REVERT: C 310 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7466 (mtmm) REVERT: C 645 MET cc_start: 0.8379 (mmm) cc_final: 0.8028 (mmm) REVERT: C 920 GLN cc_start: 0.7456 (mp10) cc_final: 0.6771 (mp10) REVERT: C 1111 LYS cc_start: 0.7785 (tmtm) cc_final: 0.7318 (tmmt) outliers start: 13 outliers final: 7 residues processed: 132 average time/residue: 1.2730 time to fit residues: 184.3186 Evaluate side-chains 123 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 930 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 50 GLN C 537 GLN ** C 696 ASN ** 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 = 0.3655 r_free = 0.3655 target = 0.125241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091808 restraints weight = 50668.505| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.89 r_work: 0.3025 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13258 Z= 0.210 Angle : 0.544 7.944 17903 Z= 0.293 Chirality : 0.040 0.149 1958 Planarity : 0.004 0.055 2320 Dihedral : 5.691 83.094 1782 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.84 % Allowed : 11.26 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1583 helix: 1.88 (0.17), residues: 885 sheet: 0.34 (0.49), residues: 99 loop : -0.39 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.014 0.002 TYR C 383 PHE 0.023 0.002 PHE A 475 TRP 0.009 0.002 TRP A 277 HIS 0.007 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (13258) covalent geometry : angle 0.54401 / 0.29 (17903) hydrogen bonds : bond 0.05845 / 3.87 ( 712) hydrogen bonds : angle 4.30549 / 3.10 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 773 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 72 MET cc_start: 0.6564 (mtp) cc_final: 0.6311 (mtp) REVERT: C 310 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7489 (mtmt) REVERT: C 645 MET cc_start: 0.8451 (mmm) cc_final: 0.8192 (mmm) REVERT: C 920 GLN cc_start: 0.7515 (mp10) cc_final: 0.6871 (mp10) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 1.2751 time to fit residues: 170.7211 Evaluate side-chains 122 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 930 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 28 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 153 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN A 733 ASN B 50 GLN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093473 restraints weight = 50482.303| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.79 r_work: 0.3050 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13258 Z= 0.152 Angle : 0.506 7.825 17903 Z= 0.270 Chirality : 0.037 0.143 1958 Planarity : 0.004 0.054 2320 Dihedral : 5.516 80.296 1782 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.70 % Allowed : 11.61 % Favored : 87.68 % 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: 1.55 (0.21), residues: 1583 helix: 2.05 (0.17), residues: 883 sheet: 0.29 (0.50), residues: 94 loop : -0.35 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.012 0.001 TYR C 383 PHE 0.023 0.002 PHE C 719 TRP 0.008 0.001 TRP A 277 HIS 0.006 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (13258) covalent geometry : angle 0.50566 / 0.27 (17903) hydrogen bonds : bond 0.05090 / 3.36 ( 712) hydrogen bonds : angle 4.18235 / 3.01 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9156.25 seconds wall clock time: 155 minutes 25.79 seconds (9325.79 seconds total)