Starting phenix.real_space_refine on Thu Mar 5 22:57:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mir_23862/03_2026/7mir_23862_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mir_23862/03_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_23862/03_2026/7mir_23862_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mir_23862/03_2026/7mir_23862_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mir_23862/03_2026/7mir_23862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mir_23862/03_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-5986/lib/python3.9/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: 3.86, 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: 1.94 Conformation dependent library (CDL) restraints added in 778.8 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: 0.65 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: 5.59 Time building geometry restraints manager: 2.65 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: 6.000 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.040 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:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 covalent geometry : bond 0.00304 (13258) covalent geometry : angle 0.49946 (17903) hydrogen bonds : bond 0.11935 ( 712) hydrogen bonds : angle 5.17645 ( 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 : 0.607 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: 1.3911 time to fit residues: 251.7844 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 : 0.595 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.126136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.093547 restraints weight = 51096.124| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.81 r_work: 0.3050 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0971 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 : 0.529 7.410 17903 Z= 0.283 Chirality : 0.039 0.171 1958 Planarity : 0.004 0.042 2320 Dihedral : 5.814 85.285 1782 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.49 % Allowed : 6.69 % Favored : 92.82 % 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: 0.57 (0.50), residues: 93 loop : -0.31 (0.25), residues: 608 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 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS C 797 Details of bonding type rmsd covalent geometry : bond 0.00420 (13258) covalent geometry : angle 0.52891 (17903) hydrogen bonds : bond 0.05596 ( 712) hydrogen bonds : angle 4.44082 ( 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 : 0.700 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7875 (ttm170) outliers start: 7 outliers final: 6 residues processed: 140 average time/residue: 1.3952 time to fit residues: 211.6610 Evaluate side-chains 130 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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: 5.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 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: 0.4980 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3675 r_free = 0.3675 target = 0.126210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094974 restraints weight = 52831.900| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.74 r_work: 0.3084 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13258 Z= 0.174 Angle : 0.521 7.786 17903 Z= 0.278 Chirality : 0.038 0.178 1958 Planarity : 0.007 0.276 2320 Dihedral : 5.717 82.475 1782 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.99 % Allowed : 8.09 % Favored : 90.92 % 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: 1.50 (0.21), residues: 1583 helix: 1.98 (0.17), residues: 884 sheet: 0.33 (0.50), residues: 94 loop : -0.35 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 127 TYR 0.014 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 covalent geometry : bond 0.00401 (13258) covalent geometry : angle 0.52109 (17903) hydrogen bonds : bond 0.05493 ( 712) hydrogen bonds : angle 4.33352 ( 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 144 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7761 (ttm170) REVERT: A 767 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: B 78 LYS cc_start: 0.7129 (tppt) cc_final: 0.6870 (mptt) REVERT: C 813 MET cc_start: 0.8228 (ptm) cc_final: 0.8000 (ptm) outliers start: 14 outliers final: 6 residues processed: 138 average time/residue: 1.5278 time to fit residues: 227.5168 Evaluate side-chains 129 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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: 0.0040 chunk 139 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 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: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3689 r_free = 0.3689 target = 0.127304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096264 restraints weight = 52487.424| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.74 r_work: 0.3111 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13258 Z= 0.125 Angle : 0.483 6.931 17903 Z= 0.255 Chirality : 0.037 0.149 1958 Planarity : 0.003 0.042 2320 Dihedral : 5.379 78.658 1782 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.70 % Allowed : 9.36 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.21), residues: 1583 helix: 2.20 (0.17), residues: 884 sheet: 0.29 (0.49), residues: 98 loop : -0.32 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.011 0.001 TYR C 383 PHE 0.023 0.001 PHE C 719 TRP 0.006 0.001 TRP A 277 HIS 0.004 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00280 (13258) covalent geometry : angle 0.48261 (17903) hydrogen bonds : bond 0.04723 ( 712) hydrogen bonds : angle 4.16004 ( 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 138 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7772 (ttm170) REVERT: A 773 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7995 (mp) REVERT: B 78 LYS cc_start: 0.7109 (tppt) cc_final: 0.6840 (mptt) REVERT: C 813 MET cc_start: 0.8152 (ptm) cc_final: 0.7910 (ptm) outliers start: 10 outliers final: 2 residues processed: 133 average time/residue: 1.4721 time to fit residues: 212.4184 Evaluate side-chains 122 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 555 LEU 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: 1.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 149 optimal weight: 0.1980 chunk 146 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3685 r_free = 0.3685 target = 0.126967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095888 restraints weight = 52521.812| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.75 r_work: 0.3109 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13258 Z= 0.135 Angle : 0.486 7.188 17903 Z= 0.258 Chirality : 0.037 0.160 1958 Planarity : 0.004 0.054 2320 Dihedral : 5.343 78.280 1782 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.91 % Allowed : 9.71 % Favored : 89.37 % 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: 1.74 (0.21), residues: 1583 helix: 2.23 (0.17), residues: 884 sheet: 0.21 (0.49), residues: 99 loop : -0.30 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 127 TYR 0.011 0.001 TYR C 383 PHE 0.022 0.001 PHE C 719 TRP 0.006 0.001 TRP A 277 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00307 (13258) covalent geometry : angle 0.48628 (17903) hydrogen bonds : bond 0.04842 ( 712) hydrogen bonds : angle 4.12602 ( 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 136 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7786 (ttm170) REVERT: A 767 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: A 773 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 72 MET cc_start: 0.6577 (mtp) cc_final: 0.6101 (mtp) REVERT: B 78 LYS cc_start: 0.7101 (tppt) cc_final: 0.6824 (mptt) REVERT: B 127 ARG cc_start: 0.6421 (ttm-80) cc_final: 0.6090 (tmm160) REVERT: C 310 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7381 (mtmm) REVERT: C 813 MET cc_start: 0.8074 (ptm) cc_final: 0.7833 (ptm) REVERT: C 920 GLN cc_start: 0.7453 (mp10) cc_final: 0.6874 (mp10) outliers start: 13 outliers final: 5 residues processed: 132 average time/residue: 1.4283 time to fit residues: 204.8315 Evaluate side-chains 127 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 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 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: 1.9990 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: 4.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3661 r_free = 0.3661 target = 0.125207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093855 restraints weight = 52851.530| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.75 r_work: 0.3061 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1464 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= 0.213 Angle : 0.551 8.084 17903 Z= 0.296 Chirality : 0.040 0.199 1958 Planarity : 0.004 0.042 2320 Dihedral : 5.651 83.161 1782 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.91 % Allowed : 10.27 % Favored : 88.81 % 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: 0.42 (0.49), residues: 99 loop : -0.38 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.014 0.002 TYR C 383 PHE 0.023 0.002 PHE A 475 TRP 0.008 0.002 TRP A 277 HIS 0.007 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00497 (13258) covalent geometry : angle 0.55073 (17903) hydrogen bonds : bond 0.05960 ( 712) hydrogen bonds : angle 4.32603 ( 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 131 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7710 (ttm170) REVERT: A 773 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 78 LYS cc_start: 0.7093 (tppt) cc_final: 0.6879 (mptt) REVERT: B 127 ARG cc_start: 0.6515 (ttm-80) cc_final: 0.6086 (tmm160) REVERT: C 310 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7424 (mtmt) REVERT: C 920 GLN cc_start: 0.7482 (mp10) cc_final: 0.6890 (mp10) outliers start: 13 outliers final: 8 residues processed: 127 average time/residue: 1.4994 time to fit residues: 205.8943 Evaluate side-chains 124 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3683 r_free = 0.3683 target = 0.126865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095675 restraints weight = 52554.164| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.73 r_work: 0.3094 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13258 Z= 0.133 Angle : 0.494 7.560 17903 Z= 0.261 Chirality : 0.037 0.152 1958 Planarity : 0.004 0.039 2320 Dihedral : 5.398 79.351 1782 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.99 % Allowed : 10.70 % Favored : 88.32 % 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: 2.14 (0.18), residues: 885 sheet: 0.33 (0.51), residues: 94 loop : -0.36 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.014 0.001 TYR C 911 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 covalent geometry : bond 0.00298 (13258) covalent geometry : angle 0.49351 (17903) hydrogen bonds : bond 0.04834 ( 712) hydrogen bonds : angle 4.14475 ( 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 136 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7782 (ttm170) REVERT: A 767 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: A 773 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8007 (mp) REVERT: B 72 MET cc_start: 0.6546 (mtp) cc_final: 0.6341 (mtp) REVERT: B 78 LYS cc_start: 0.7103 (tppt) cc_final: 0.6898 (tptt) REVERT: B 125 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6797 (mmt) REVERT: B 127 ARG cc_start: 0.6501 (ttm-80) cc_final: 0.6056 (tmm160) REVERT: C 310 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7399 (mtmm) REVERT: C 920 GLN cc_start: 0.7561 (mp10) cc_final: 0.6976 (mp10) REVERT: C 1111 LYS cc_start: 0.7788 (tmtm) cc_final: 0.7207 (tmmt) outliers start: 14 outliers final: 6 residues processed: 131 average time/residue: 1.4293 time to fit residues: 203.2985 Evaluate side-chains 124 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- 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: 0.6980 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 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: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.125250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.091656 restraints weight = 50841.165| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.84 r_work: 0.3025 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13258 Z= 0.207 Angle : 0.547 7.948 17903 Z= 0.293 Chirality : 0.040 0.194 1958 Planarity : 0.004 0.052 2320 Dihedral : 5.637 82.770 1782 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.20 % Allowed : 10.49 % Favored : 88.32 % 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: 1.44 (0.21), residues: 1583 helix: 1.91 (0.17), residues: 884 sheet: 0.40 (0.49), residues: 99 loop : -0.36 (0.25), residues: 600 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 0.008 0.002 TRP A 277 HIS 0.006 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00482 (13258) covalent geometry : angle 0.54651 (17903) hydrogen bonds : bond 0.05817 ( 712) hydrogen bonds : angle 4.30424 ( 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 134 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7691 (ttm170) REVERT: A 773 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8060 (mp) REVERT: B 78 LYS cc_start: 0.7085 (tppt) cc_final: 0.6769 (mptt) REVERT: B 125 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6821 (mmt) REVERT: C 310 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7479 (mtmt) REVERT: C 870 ASP cc_start: 0.7343 (t70) cc_final: 0.6987 (t70) REVERT: C 920 GLN cc_start: 0.7564 (mp10) cc_final: 0.6963 (mp10) REVERT: C 1111 LYS cc_start: 0.7804 (tmtm) cc_final: 0.7339 (tmmt) outliers start: 17 outliers final: 8 residues processed: 128 average time/residue: 1.4515 time to fit residues: 201.6570 Evaluate side-chains 123 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 96 optimal weight: 1.9990 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: 1.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3668 r_free = 0.3668 target = 0.126193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092781 restraints weight = 50612.774| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.85 r_work: 0.3042 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13258 Z= 0.164 Angle : 0.518 7.783 17903 Z= 0.274 Chirality : 0.038 0.170 1958 Planarity : 0.004 0.050 2320 Dihedral : 5.516 80.783 1782 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.06 % Allowed : 10.91 % 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: 1.53 (0.21), residues: 1583 helix: 2.01 (0.17), residues: 885 sheet: 0.31 (0.50), residues: 94 loop : -0.35 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.014 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 covalent geometry : bond 0.00378 (13258) covalent geometry : angle 0.51783 (17903) hydrogen bonds : bond 0.05236 ( 712) hydrogen bonds : angle 4.21390 ( 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: 15 poor density : 119 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7695 (ttm170) REVERT: A 773 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8051 (mp) REVERT: B 125 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6817 (mmt) REVERT: B 127 ARG cc_start: 0.6438 (ttm-80) cc_final: 0.6019 (tmm160) REVERT: C 310 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7457 (mtmm) REVERT: C 920 GLN cc_start: 0.7512 (mp10) cc_final: 0.6874 (mp10) REVERT: C 1111 LYS cc_start: 0.7794 (tmtm) cc_final: 0.7350 (tmmt) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 1.3993 time to fit residues: 196.0693 Evaluate side-chains 129 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 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=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: 0.5980 chunk 102 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3671 r_free = 0.3671 target = 0.126431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093418 restraints weight = 50591.252| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.82 r_work: 0.3049 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13258 Z= 0.156 Angle : 0.514 8.084 17903 Z= 0.272 Chirality : 0.038 0.169 1958 Planarity : 0.004 0.051 2320 Dihedral : 5.483 80.531 1782 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.99 % Allowed : 11.12 % 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: 1.53 (0.21), residues: 1583 helix: 2.04 (0.18), residues: 878 sheet: 0.28 (0.50), residues: 94 loop : -0.35 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 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 covalent geometry : bond 0.00360 (13258) covalent geometry : angle 0.51361 (17903) hydrogen bonds : bond 0.05173 ( 712) hydrogen bonds : angle 4.18466 ( 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: 14 poor density : 120 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7687 (ttm170) REVERT: A 767 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: A 773 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8018 (mp) REVERT: B 125 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6787 (mmt) REVERT: B 127 ARG cc_start: 0.6462 (ttm-80) cc_final: 0.6010 (tmm160) REVERT: C 310 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7459 (mtmm) REVERT: C 920 GLN cc_start: 0.7564 (mp10) cc_final: 0.6891 (mp10) REVERT: C 1111 LYS cc_start: 0.7833 (tmtm) cc_final: 0.7364 (tmmt) outliers start: 14 outliers final: 7 residues processed: 130 average time/residue: 1.3376 time to fit residues: 188.6891 Evaluate side-chains 129 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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=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: 0.8980 chunk 103 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3671 r_free = 0.3671 target = 0.126420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093392 restraints weight = 50448.803| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.80 r_work: 0.3049 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13258 Z= 0.159 Angle : 0.520 8.516 17903 Z= 0.275 Chirality : 0.038 0.171 1958 Planarity : 0.004 0.051 2320 Dihedral : 5.476 80.257 1782 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.91 % Allowed : 11.26 % Favored : 87.83 % 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: 2.02 (0.18), residues: 878 sheet: 0.39 (0.49), residues: 99 loop : -0.34 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.016 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 covalent geometry : bond 0.00366 (13258) covalent geometry : angle 0.51960 (17903) hydrogen bonds : bond 0.05172 ( 712) hydrogen bonds : angle 4.18936 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9221.34 seconds wall clock time: 156 minutes 14.70 seconds (9374.70 seconds total)