Starting phenix.real_space_refine on Sun Jul 5 06:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mir_23862/07_2026/7mir_23862_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mir_23862/07_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_23862/07_2026/7mir_23862_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mir_23862/07_2026/7mir_23862_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mir_23862/07_2026/7mir_23862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mir_23862/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 4.27, per 1000 atoms: 0.17 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: 2.39 Conformation dependent library (CDL) restraints added in 762.1 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: 6.14 Time building geometry restraints manager: 3.38 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: 46830 2.46 - 4.91: 99 4.91 - 7.37: 5 7.37 - 9.82: 6 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: 11110 17.53 - 35.07: 845 35.07 - 52.60: 208 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: 1666 0.050 - 0.100: 243 0.100 - 0.150: 46 0.150 - 0.200: 1 0.200 - 0.250: 2 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=" C3' AMP A 901 " pdb=" C2' AMP A 901 " pdb=" C4' AMP A 901 " pdb=" O3' AMP A 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.19e+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 ... (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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.810 Find NCS groups from input model: 0.100 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- 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= 0.143 Angle : 0.499 12.277 17903 Z= 0.264 Chirality : 0.037 0.250 1958 Planarity : 0.003 0.045 2320 Dihedral : 14.441 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 0.00304 / 0.14 (13258) covalent geometry : angle 0.49946 / 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 : 0.743 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: 1.4004 time to fit residues: 255.2569 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 : 0.673 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.126107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091776 restraints weight = 50782.500| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.77 r_work: 0.3042 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13258 Z= 0.182 Angle : 0.527 7.740 17903 Z= 0.281 Chirality : 0.039 0.173 1958 Planarity : 0.004 0.043 2320 Dihedral : 5.821 86.095 1782 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.49 % Allowed : 6.76 % Favored : 92.75 % 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: 1.60 (0.21), residues: 1583 helix: 2.05 (0.17), residues: 882 sheet: 0.49 (0.51), residues: 94 loop : -0.29 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 127 TYR 0.014 0.002 TYR C 383 PHE 0.024 0.002 PHE C 719 TRP 0.008 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 0.52701 / 0.28 (17903) hydrogen bonds : bond 0.05630 / 3.71 ( 712) hydrogen bonds : angle 4.44046 / 3.21 ( 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 142 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7874 (ttm170) outliers start: 7 outliers final: 6 residues processed: 140 average time/residue: 1.3313 time to fit residues: 204.2113 Evaluate side-chains 129 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 B residue 127 ARG 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: 4.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 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: 0.3980 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.125443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091145 restraints weight = 50934.420| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.77 r_work: 0.3031 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13258 Z= 0.188 Angle : 0.532 7.783 17903 Z= 0.285 Chirality : 0.039 0.184 1958 Planarity : 0.007 0.275 2320 Dihedral : 5.762 82.782 1782 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.99 % Allowed : 8.23 % Favored : 90.78 % 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: 1.45 (0.21), residues: 1583 helix: 1.93 (0.17), residues: 884 sheet: 0.34 (0.50), residues: 94 loop : -0.36 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG B 127 TYR 0.015 0.002 TYR C 383 PHE 0.023 0.002 PHE C 719 TRP 0.008 0.001 TRP A 277 HIS 0.004 0.001 HIS C 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (13258) covalent geometry : angle 0.53155 / 0.28 (17903) hydrogen bonds : bond 0.05687 / 3.76 ( 712) hydrogen bonds : angle 4.36628 / 3.15 ( 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 143 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: A 767 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: B 65 ASP cc_start: 0.8587 (p0) cc_final: 0.8374 (p0) REVERT: B 78 LYS cc_start: 0.7120 (tppt) cc_final: 0.6865 (mptt) REVERT: C 920 GLN cc_start: 0.7158 (mp10) cc_final: 0.6850 (mp10) outliers start: 14 outliers final: 6 residues processed: 137 average time/residue: 1.3708 time to fit residues: 204.9716 Evaluate side-chains 130 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 139 optimal weight: 0.0470 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 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: 1.6086 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.126272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095051 restraints weight = 52346.977| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.71 r_work: 0.3095 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13258 Z= 0.165 Angle : 0.512 7.507 17903 Z= 0.272 Chirality : 0.038 0.173 1958 Planarity : 0.004 0.043 2320 Dihedral : 5.530 80.875 1782 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.99 % Allowed : 9.36 % Favored : 89.66 % 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: 1.49 (0.21), residues: 1583 helix: 1.99 (0.17), residues: 884 sheet: 0.29 (0.50), residues: 94 loop : -0.37 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.013 0.002 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 0.00381 / 0.17 (13258) covalent geometry : angle 0.51198 / 0.27 (17903) hydrogen bonds : bond 0.05333 / 3.52 ( 712) hydrogen bonds : angle 4.26624 / 3.08 ( 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 145 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7731 (ttm170) REVERT: A 767 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: A 773 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8001 (mp) REVERT: B 7 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: B 78 LYS cc_start: 0.7109 (tppt) cc_final: 0.6837 (mptt) REVERT: B 127 ARG cc_start: 0.5799 (OUTLIER) cc_final: 0.5594 (tmm160) REVERT: C 310 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7411 (mtmm) REVERT: C 920 GLN cc_start: 0.7354 (mp10) cc_final: 0.7092 (mp10) outliers start: 14 outliers final: 5 residues processed: 140 average time/residue: 1.2750 time to fit residues: 195.5308 Evaluate side-chains 131 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 7 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 127 ARG 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: 0.9990 chunk 126 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.125512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090790 restraints weight = 50544.955| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.77 r_work: 0.3029 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13258 Z= 0.192 Angle : 0.535 7.872 17903 Z= 0.287 Chirality : 0.039 0.188 1958 Planarity : 0.004 0.047 2320 Dihedral : 5.614 82.287 1782 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.20 % Allowed : 10.13 % Favored : 88.67 % 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: 1.41 (0.21), residues: 1583 helix: 1.91 (0.17), residues: 884 sheet: 0.28 (0.50), residues: 94 loop : -0.39 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.013 0.002 TYR C 383 PHE 0.023 0.002 PHE C 719 TRP 0.009 0.001 TRP A 277 HIS 0.006 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (13258) covalent geometry : angle 0.53535 / 0.29 (17903) hydrogen bonds : bond 0.05691 / 3.76 ( 712) hydrogen bonds : angle 4.30556 / 3.11 ( 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 141 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7704 (ttm170) REVERT: A 767 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: A 773 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 7 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: B 72 MET cc_start: 0.6517 (mtp) cc_final: 0.6300 (mtp) REVERT: B 127 ARG cc_start: 0.6105 (tmm-80) cc_final: 0.5795 (tmm160) REVERT: C 310 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7494 (mtmt) REVERT: C 920 GLN cc_start: 0.7365 (mp10) cc_final: 0.7044 (mp10) REVERT: C 1111 LYS cc_start: 0.7735 (tmtm) cc_final: 0.7328 (tmmt) REVERT: C 1114 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6132 (tp30) outliers start: 17 outliers final: 8 residues processed: 136 average time/residue: 1.4162 time to fit residues: 210.2946 Evaluate side-chains 132 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 78 optimal weight: 3.9990 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: 0.9980 chunk 136 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.125520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.090773 restraints weight = 50762.797| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.78 r_work: 0.3028 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1479 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= 0.195 Angle : 0.537 7.753 17903 Z= 0.287 Chirality : 0.039 0.183 1958 Planarity : 0.004 0.050 2320 Dihedral : 5.625 82.203 1782 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.48 % Allowed : 10.49 % Favored : 88.04 % 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: 1.37 (0.21), residues: 1583 helix: 1.89 (0.17), residues: 884 sheet: 0.28 (0.50), residues: 94 loop : -0.43 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.013 0.002 TYR C 383 PHE 0.023 0.002 PHE C 719 TRP 0.009 0.001 TRP A 277 HIS 0.007 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (13258) covalent geometry : angle 0.53739 / 0.29 (17903) hydrogen bonds : bond 0.05678 / 3.75 ( 712) hydrogen bonds : angle 4.30548 / 3.11 ( 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 145 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7690 (ttm170) REVERT: A 773 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8012 (mp) REVERT: B 7 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: B 125 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6854 (mmt) REVERT: B 127 ARG cc_start: 0.6085 (tmm-80) cc_final: 0.5775 (tmm160) REVERT: C 310 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7498 (mtmt) REVERT: C 920 GLN cc_start: 0.7452 (mp10) cc_final: 0.7072 (mp10) REVERT: C 1111 LYS cc_start: 0.7781 (tmtm) cc_final: 0.7365 (tmmt) outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 1.3694 time to fit residues: 205.1529 Evaluate side-chains 135 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 B residue 125 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.126123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091450 restraints weight = 50476.975| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.77 r_work: 0.3039 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13258 Z= 0.158 Angle : 0.513 7.358 17903 Z= 0.272 Chirality : 0.038 0.169 1958 Planarity : 0.004 0.048 2320 Dihedral : 5.528 80.795 1782 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.34 % Allowed : 10.49 % Favored : 88.18 % 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: 1.54 (0.21), residues: 1583 helix: 2.04 (0.17), residues: 883 sheet: 0.28 (0.50), residues: 94 loop : -0.36 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.013 0.002 TYR C 911 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 0.00361 / 0.16 (13258) covalent geometry : angle 0.51300 / 0.27 (17903) hydrogen bonds : bond 0.05220 / 3.44 ( 712) hydrogen bonds : angle 4.21573 / 3.04 ( 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 145 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7691 (ttm170) REVERT: A 773 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 7 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: B 72 MET cc_start: 0.6592 (mtp) cc_final: 0.6355 (mtm) REVERT: C 310 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7471 (mtmm) REVERT: C 920 GLN cc_start: 0.7483 (mp10) cc_final: 0.7085 (mp10) REVERT: C 1111 LYS cc_start: 0.7756 (tmtm) cc_final: 0.7320 (tmmt) outliers start: 19 outliers final: 9 residues processed: 140 average time/residue: 1.4094 time to fit residues: 215.4475 Evaluate side-chains 131 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 64 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** C 920 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.091725 restraints weight = 50740.465| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.88 r_work: 0.3026 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13258 Z= 0.208 Angle : 0.554 7.914 17903 Z= 0.296 Chirality : 0.040 0.195 1958 Planarity : 0.004 0.048 2320 Dihedral : 5.695 82.772 1782 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.48 % Allowed : 10.98 % Favored : 87.54 % 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: 1.34 (0.21), residues: 1583 helix: 1.83 (0.17), residues: 885 sheet: 0.37 (0.49), residues: 99 loop : -0.41 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 127 TYR 0.014 0.002 TYR C 383 PHE 0.023 0.002 PHE C 719 TRP 0.008 0.002 TRP A 277 HIS 0.007 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (13258) covalent geometry : angle 0.55392 / 0.30 (17903) hydrogen bonds : bond 0.05863 / 3.88 ( 712) hydrogen bonds : angle 4.32282 / 3.12 ( 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 140 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7704 (ttm170) REVERT: A 773 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 7 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6684 (tm-30) REVERT: C 310 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7487 (mtmt) REVERT: C 416 GLN cc_start: 0.7346 (tp40) cc_final: 0.7038 (tp40) REVERT: C 920 GLN cc_start: 0.7532 (mp-120) cc_final: 0.7031 (mp10) outliers start: 21 outliers final: 11 residues processed: 136 average time/residue: 1.3593 time to fit residues: 202.8091 Evaluate side-chains 128 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 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 600 VAL Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 698 SER 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: 1.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.125524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.091323 restraints weight = 50540.168| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.75 r_work: 0.3035 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13258 Z= 0.164 Angle : 0.515 7.573 17903 Z= 0.273 Chirality : 0.038 0.166 1958 Planarity : 0.004 0.047 2320 Dihedral : 5.550 80.762 1782 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.13 % Allowed : 11.40 % Favored : 87.47 % 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: 1.49 (0.21), residues: 1583 helix: 2.00 (0.17), residues: 885 sheet: 0.26 (0.50), residues: 94 loop : -0.40 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 127 TYR 0.015 0.002 TYR C 911 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 0.00377 / 0.16 (13258) covalent geometry : angle 0.51496 / 0.27 (17903) hydrogen bonds : bond 0.05265 / 3.47 ( 712) hydrogen bonds : angle 4.21952 / 3.04 ( 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 135 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7703 (ttm170) REVERT: A 773 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8076 (mp) REVERT: B 7 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: C 310 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7459 (mtmm) REVERT: C 920 GLN cc_start: 0.7657 (mp-120) cc_final: 0.7164 (mp10) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 1.3585 time to fit residues: 196.5738 Evaluate side-chains 127 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 698 SER 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: 0.8980 chunk 102 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 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: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.125886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091730 restraints weight = 50512.413| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.75 r_work: 0.3043 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1566 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= 0.147 Angle : 0.509 7.950 17903 Z= 0.269 Chirality : 0.037 0.165 1958 Planarity : 0.004 0.046 2320 Dihedral : 5.475 80.244 1782 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.91 % Allowed : 11.75 % Favored : 87.33 % 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: 2.07 (0.17), residues: 885 sheet: 0.36 (0.51), residues: 92 loop : -0.33 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 127 TYR 0.015 0.002 TYR C 911 PHE 0.023 0.001 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 0.00336 / 0.15 (13258) covalent geometry : angle 0.50896 / 0.27 (17903) hydrogen bonds : bond 0.05038 / 3.32 ( 712) hydrogen bonds : angle 4.17479 / 3.01 ( 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 134 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 7 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: C 310 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7471 (mtmm) REVERT: C 920 GLN cc_start: 0.7872 (mp-120) cc_final: 0.7269 (mp10) outliers start: 13 outliers final: 8 residues processed: 132 average time/residue: 1.3778 time to fit residues: 199.4379 Evaluate side-chains 129 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 GLU 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 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 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: 4.9990 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 153 optimal weight: 0.0670 chunk 17 optimal weight: 0.9990 chunk 115 optimal weight: 0.0670 chunk 148 optimal weight: 2.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.127827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096891 restraints weight = 52153.219| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.72 r_work: 0.3115 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13258 Z= 0.111 Angle : 0.474 7.737 17903 Z= 0.249 Chirality : 0.036 0.142 1958 Planarity : 0.004 0.046 2320 Dihedral : 5.265 77.720 1782 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.56 % Allowed : 12.32 % Favored : 87.12 % 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: 1.78 (0.21), residues: 1583 helix: 2.23 (0.18), residues: 889 sheet: 0.32 (0.51), residues: 92 loop : -0.27 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 127 TYR 0.016 0.001 TYR C 911 PHE 0.023 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 0.00246 / 0.11 (13258) covalent geometry : angle 0.47440 / 0.25 (17903) hydrogen bonds : bond 0.04341 / 2.85 ( 712) hydrogen bonds : angle 4.03671 / 2.91 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9706.15 seconds wall clock time: 165 minutes 5.89 seconds (9905.89 seconds total)