Starting phenix.real_space_refine on Sat Jul 4 06:26:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hm6_52287/07_2026/9hm6_52287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hm6_52287/07_2026/9hm6_52287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hm6_52287/07_2026/9hm6_52287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hm6_52287/07_2026/9hm6_52287_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hm6_52287/07_2026/9hm6_52287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hm6_52287/07_2026/9hm6_52287.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 80 5.49 5 S 20 5.16 5 C 5767 2.51 5 N 1645 2.21 5 O 2044 1.98 5 H 8795 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 18351 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 15793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 15793 Classifications: {'peptide': 960} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 940} Chain breaks: 3 Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1506 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 24, 'rna3p_pyr': 19} Link IDs: {'rna2p': 4, 'rna3p': 42} Chain: "C" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1052 Classifications: {'RNA': 33} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 32} Time building chain proxies: 3.48, per 1000 atoms: 0.19 Number of scatterers: 18351 At special positions: 0 Unit cell: (98.28, 107.38, 131.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 80 15.00 O 2044 8.00 N 1645 7.00 C 5767 6.00 H 8795 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 809.1 milliseconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 54.1% alpha, 12.0% beta 28 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.559A pdb=" N LYS A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 4.252A pdb=" N GLU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 4.616A pdb=" N PHE A 247 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 250 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 Processing helix chain 'A' and resid 292 through 314 Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 332 through 355 removed outlier: 3.762A pdb=" N PHE A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.725A pdb=" N PHE A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 415 removed outlier: 4.277A pdb=" N GLN A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 removed outlier: 4.280A pdb=" N ALA A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.794A pdb=" N GLU A 484 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.124A pdb=" N LYS A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 493' Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 516 through 530 removed outlier: 3.560A pdb=" N LYS A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 540 through 548 Processing helix chain 'A' and resid 555 through 568 removed outlier: 3.758A pdb=" N PHE A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.689A pdb=" N LYS A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.640A pdb=" N GLN A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP A 613 " --> pdb=" O HIS A 609 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.785A pdb=" N LYS A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 646 removed outlier: 3.624A pdb=" N LYS A 645 " --> pdb=" O LYS A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 698 removed outlier: 3.711A pdb=" N LYS A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.539A pdb=" N TYR A 776 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 790 through 801 Processing helix chain 'A' and resid 827 through 848 removed outlier: 4.539A pdb=" N LEU A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 876 through 878 No H-bonds generated for 'chain 'A' and resid 876 through 878' Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 887 through 900 Processing helix chain 'A' and resid 908 through 919 Processing helix chain 'A' and resid 952 through 956 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 968 through 982 removed outlier: 3.872A pdb=" N TYR A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 980 " --> pdb=" O ILE A 976 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 981 " --> pdb=" O ASP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 986 Processing helix chain 'A' and resid 989 through 1024 removed outlier: 3.993A pdb=" N LEU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1064 removed outlier: 3.651A pdb=" N ASN A1064 " --> pdb=" O GLN A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 Processing helix chain 'A' and resid 1135 through 1155 removed outlier: 4.216A pdb=" N ILE A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 569 through 574 removed outlier: 5.760A pdb=" N PHE A 467 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ALA A 425 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 437 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS A 434 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 593 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A 590 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR A 664 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 669 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU A 633 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER A 671 " --> pdb=" O ASN A 631 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN A 631 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 212 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N TYR A 638 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N TYR A 423 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS A 213 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA A 425 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER A 215 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ILE A 427 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 810 removed outlier: 3.584A pdb=" N LEU A 810 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 721 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A1030 " --> pdb=" O PHE A 709 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A1032 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A1098 " --> pdb=" O LYS A1031 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 748 through 753 Processing sheet with id=AA5, first strand: chain 'A' and resid 759 through 761 Processing sheet with id=AA6, first strand: chain 'A' and resid 816 through 818 Processing sheet with id=AA7, first strand: chain 'A' and resid 856 through 858 385 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 2.41 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: 4529 1.03 - 1.23: 4474 1.23 - 1.42: 4935 1.42 - 1.62: 4718 1.62 - 1.81: 30 Bond restraints: 18686 Sorted by residual: bond pdb=" CE1 HIS A 661 " pdb=" NE2 HIS A 661 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.88e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.86e+01 bond pdb=" CE1 HIS A 838 " pdb=" NE2 HIS A 838 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.84e+01 bond pdb=" CE1 HIS A 673 " pdb=" NE2 HIS A 673 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.80e+01 bond pdb=" ND1 HIS A 849 " pdb=" CE1 HIS A 849 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.74e+01 ... (remaining 18681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 24715 2.55 - 5.11: 5897 5.11 - 7.66: 2613 7.66 - 10.22: 451 10.22 - 12.77: 83 Bond angle restraints: 33759 Sorted by residual: angle pdb=" N6 A C 13 " pdb=" C6 A C 13 " pdb=" N1 A C 13 " ideal model delta sigma weight residual 118.60 112.07 6.53 6.00e-01 2.78e+00 1.19e+02 angle pdb=" N6 A B 38 " pdb=" C6 A B 38 " pdb=" N1 A B 38 " ideal model delta sigma weight residual 118.60 112.33 6.27 6.00e-01 2.78e+00 1.09e+02 angle pdb=" N6 A B 58 " pdb=" C6 A B 58 " pdb=" N1 A B 58 " ideal model delta sigma weight residual 118.60 112.54 6.06 6.00e-01 2.78e+00 1.02e+02 angle pdb=" N6 A C 37 " pdb=" C6 A C 37 " pdb=" N1 A C 37 " ideal model delta sigma weight residual 118.60 112.78 5.82 6.00e-01 2.78e+00 9.40e+01 angle pdb=" N6 A C 10 " pdb=" C6 A C 10 " pdb=" N1 A C 10 " ideal model delta sigma weight residual 118.60 112.82 5.78 6.00e-01 2.78e+00 9.28e+01 ... (remaining 33754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 8421 35.76 - 71.51: 343 71.51 - 107.27: 31 107.27 - 143.02: 9 143.02 - 178.78: 9 Dihedral angle restraints: 8813 sinusoidal: 5469 harmonic: 3344 Sorted by residual: dihedral pdb=" C5' G B 37 " pdb=" C4' G B 37 " pdb=" C3' G B 37 " pdb=" O3' G B 37 " ideal model delta sinusoidal sigma weight residual 147.00 78.37 68.63 1 8.00e+00 1.56e-02 9.53e+01 dihedral pdb=" C5' U B 36 " pdb=" C4' U B 36 " pdb=" C3' U B 36 " pdb=" O3' U B 36 " ideal model delta sinusoidal sigma weight residual 147.00 79.45 67.55 1 8.00e+00 1.56e-02 9.27e+01 dihedral pdb=" O4' U C 30 " pdb=" C1' U C 30 " pdb=" N1 U C 30 " pdb=" C2 U C 30 " ideal model delta sinusoidal sigma weight residual 200.00 40.16 159.84 1 1.50e+01 4.44e-03 8.27e+01 ... (remaining 8810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 977 0.151 - 0.301: 62 0.301 - 0.452: 95 0.452 - 0.602: 330 0.602 - 0.753: 108 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CG LEU A 310 " pdb=" CB LEU A 310 " pdb=" CD1 LEU A 310 " pdb=" CD2 LEU A 310 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CG LEU A 998 " pdb=" CB LEU A 998 " pdb=" CD1 LEU A 998 " pdb=" CD2 LEU A 998 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CB ILE A1029 " pdb=" CA ILE A1029 " pdb=" CG1 ILE A1029 " pdb=" CG2 ILE A1029 " both_signs ideal model delta sigma weight residual False 2.64 1.91 0.74 2.00e-01 2.50e+01 1.35e+01 ... (remaining 1569 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 37 " 0.431 2.00e-02 2.50e+03 1.62e-01 8.56e+02 pdb=" N9 A C 37 " -0.083 2.00e-02 2.50e+03 pdb=" C8 A C 37 " -0.096 2.00e-02 2.50e+03 pdb=" N7 A C 37 " -0.110 2.00e-02 2.50e+03 pdb=" C5 A C 37 " -0.090 2.00e-02 2.50e+03 pdb=" C6 A C 37 " 0.041 2.00e-02 2.50e+03 pdb=" N6 A C 37 " 0.273 2.00e-02 2.50e+03 pdb=" N1 A C 37 " 0.037 2.00e-02 2.50e+03 pdb=" C2 A C 37 " -0.051 2.00e-02 2.50e+03 pdb=" N3 A C 37 " -0.127 2.00e-02 2.50e+03 pdb=" C4 A C 37 " -0.144 2.00e-02 2.50e+03 pdb=" H8 A C 37 " -0.043 2.00e-02 2.50e+03 pdb=" H2 A C 37 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 36 " 0.387 2.00e-02 2.50e+03 1.63e-01 7.28e+02 pdb=" N1 C C 36 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C C 36 " -0.019 2.00e-02 2.50e+03 pdb=" O2 C C 36 " -0.268 2.00e-02 2.50e+03 pdb=" N3 C C 36 " 0.035 2.00e-02 2.50e+03 pdb=" C4 C C 36 " 0.087 2.00e-02 2.50e+03 pdb=" N4 C C 36 " 0.137 2.00e-02 2.50e+03 pdb=" C5 C C 36 " -0.020 2.00e-02 2.50e+03 pdb=" C6 C C 36 " -0.098 2.00e-02 2.50e+03 pdb=" H5 C C 36 " -0.042 2.00e-02 2.50e+03 pdb=" H6 C C 36 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " -0.365 2.00e-02 2.50e+03 1.54e-01 7.07e+02 pdb=" N1 U B 45 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U B 45 " 0.054 2.00e-02 2.50e+03 pdb=" O2 U B 45 " 0.218 2.00e-02 2.50e+03 pdb=" N3 U B 45 " -0.011 2.00e-02 2.50e+03 pdb=" C4 U B 45 " -0.087 2.00e-02 2.50e+03 pdb=" O4 U B 45 " -0.203 2.00e-02 2.50e+03 pdb=" C5 U B 45 " 0.021 2.00e-02 2.50e+03 pdb=" C6 U B 45 " 0.074 2.00e-02 2.50e+03 pdb=" H5 U B 45 " 0.074 2.00e-02 2.50e+03 pdb=" H3 U B 45 " 0.068 2.00e-02 2.50e+03 pdb=" H6 U B 45 " 0.183 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 619 2.10 - 2.72: 29261 2.72 - 3.35: 51046 3.35 - 3.97: 63520 3.97 - 4.60: 96683 Nonbonded interactions: 241129 Sorted by model distance: nonbonded pdb=" O PHE A1034 " pdb="HH12 ARG A1078 " model vdw 1.471 2.450 nonbonded pdb=" H THR A 968 " pdb=" OE1 GLU A 971 " model vdw 1.479 2.450 nonbonded pdb=" OE1 GLN A 495 " pdb=" H GLN A 495 " model vdw 1.533 2.450 nonbonded pdb=" OE1 GLU A 969 " pdb=" H GLU A 969 " model vdw 1.558 2.450 nonbonded pdb="HD21 ASN A 358 " pdb=" OE1 GLN A 361 " model vdw 1.560 2.450 ... (remaining 241124 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 group one per residue 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: 1.090 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: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.036 0.150 9891 Z= 1.865 Angle : 2.701 12.040 13683 Z= 1.921 Chirality : 0.327 0.753 1572 Planarity : 0.017 0.175 1458 Dihedral : 19.367 171.793 4292 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.14 % Favored : 92.44 % Rotamer: Outliers : 0.23 % Allowed : 4.96 % Favored : 94.81 % Cbeta Deviations : 22.98 % 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: -2.02 (0.25), residues: 952 helix: -1.31 (0.23), residues: 420 sheet: -0.06 (0.51), residues: 108 loop : -1.61 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 785 TYR 0.109 0.010 TYR A 218 PHE 0.036 0.008 PHE A 787 TRP 0.033 0.008 TRP A 613 HIS 0.006 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.03578 / 1.87 ( 9891) covalent geometry : angle 2.70089 / 1.92 (13683) hydrogen bonds : bond 0.21964 / 14.18 ( 456) hydrogen bonds : angle 7.76064 / 5.38 ( 1172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.9253 (tp40) cc_final: 0.8693 (tm-30) REVERT: A 298 ASN cc_start: 0.9484 (m110) cc_final: 0.8766 (m110) REVERT: A 679 LYS cc_start: 0.8975 (mttp) cc_final: 0.8526 (mmtt) REVERT: A 1055 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8799 (tm-30) REVERT: A 1072 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8221 (mmtt) REVERT: A 1137 ASP cc_start: 0.8255 (m-30) cc_final: 0.7631 (p0) outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 0.2469 time to fit residues: 34.6551 Evaluate side-chains 84 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN A 847 ASN A1105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.059951 restraints weight = 130689.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.062870 restraints weight = 57636.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064719 restraints weight = 35785.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.065887 restraints weight = 26753.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066543 restraints weight = 22266.981| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9891 Z= 0.226 Angle : 0.727 7.428 13683 Z= 0.442 Chirality : 0.048 0.277 1572 Planarity : 0.005 0.050 1458 Dihedral : 21.640 179.178 2259 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.04 % Favored : 92.65 % Rotamer: Outliers : 1.38 % Allowed : 6.46 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.26), residues: 952 helix: -0.22 (0.23), residues: 426 sheet: -0.09 (0.50), residues: 113 loop : -1.47 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 960 TYR 0.016 0.002 TYR A 783 PHE 0.018 0.002 PHE A1062 TRP 0.010 0.002 TRP A 897 HIS 0.006 0.002 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.23 ( 9891) covalent geometry : angle 0.72652 / 0.44 (13683) hydrogen bonds : bond 0.07927 / 5.21 ( 456) hydrogen bonds : angle 5.78937 / 4.04 ( 1172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.9151 (tp40) cc_final: 0.8610 (tm-30) REVERT: A 298 ASN cc_start: 0.9491 (m110) cc_final: 0.8828 (m110) REVERT: A 333 GLN cc_start: 0.9441 (tt0) cc_final: 0.9228 (tm-30) REVERT: A 369 LYS cc_start: 0.9621 (OUTLIER) cc_final: 0.9283 (mttm) REVERT: A 477 LYS cc_start: 0.9254 (tttt) cc_final: 0.9048 (tttt) REVERT: A 694 ASP cc_start: 0.9449 (t0) cc_final: 0.9075 (m-30) REVERT: A 1055 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8858 (tm-30) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.2314 time to fit residues: 28.0573 Evaluate side-chains 83 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 27 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN A 545 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.081296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.060293 restraints weight = 132671.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063200 restraints weight = 58081.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065008 restraints weight = 36120.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066154 restraints weight = 27188.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066847 restraints weight = 22757.569| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9891 Z= 0.167 Angle : 0.614 7.167 13683 Z= 0.377 Chirality : 0.042 0.273 1572 Planarity : 0.004 0.037 1458 Dihedral : 21.551 179.011 2259 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.93 % Favored : 92.75 % Rotamer: Outliers : 1.38 % Allowed : 8.42 % Favored : 90.20 % 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: -0.67 (0.27), residues: 952 helix: 0.39 (0.24), residues: 426 sheet: -0.07 (0.51), residues: 108 loop : -1.40 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 441 TYR 0.017 0.001 TYR A 783 PHE 0.011 0.001 PHE A 465 TRP 0.010 0.001 TRP A 897 HIS 0.005 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 ( 9891) covalent geometry : angle 0.61417 / 0.38 (13683) hydrogen bonds : bond 0.06403 / 4.21 ( 456) hydrogen bonds : angle 5.27475 / 3.68 ( 1172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.9117 (tp40) cc_final: 0.8553 (tm-30) REVERT: A 298 ASN cc_start: 0.9454 (m110) cc_final: 0.8816 (m110) REVERT: A 333 GLN cc_start: 0.9437 (tt0) cc_final: 0.9226 (tm-30) REVERT: A 369 LYS cc_start: 0.9617 (OUTLIER) cc_final: 0.9258 (mttm) REVERT: A 477 LYS cc_start: 0.9206 (tttt) cc_final: 0.8978 (tttt) REVERT: A 694 ASP cc_start: 0.9434 (t0) cc_final: 0.9082 (m-30) REVERT: A 1055 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8834 (tm-30) outliers start: 12 outliers final: 9 residues processed: 81 average time/residue: 0.2135 time to fit residues: 23.6777 Evaluate side-chains 80 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 344 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN A 782 ASN ** A1117 HIS ** 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 = 0.3699 r_free = 0.3699 target = 0.079548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058736 restraints weight = 134921.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061605 restraints weight = 59361.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063343 restraints weight = 37014.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064486 restraints weight = 28058.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.065128 restraints weight = 23453.683| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9891 Z= 0.222 Angle : 0.621 8.072 13683 Z= 0.371 Chirality : 0.041 0.352 1572 Planarity : 0.004 0.040 1458 Dihedral : 21.634 179.598 2259 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.25 % Favored : 92.44 % Rotamer: Outliers : 1.73 % Allowed : 9.00 % Favored : 89.27 % 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: -0.72 (0.27), residues: 952 helix: 0.45 (0.24), residues: 426 sheet: -0.13 (0.52), residues: 106 loop : -1.54 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 902 TYR 0.017 0.002 TYR A 783 PHE 0.016 0.002 PHE A1062 TRP 0.011 0.002 TRP A 897 HIS 0.006 0.002 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 ( 9891) covalent geometry : angle 0.62087 / 0.37 (13683) hydrogen bonds : bond 0.06152 / 4.04 ( 456) hydrogen bonds : angle 5.13753 / 3.57 ( 1172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6928 (m-40) REVERT: A 294 GLN cc_start: 0.9141 (tp40) cc_final: 0.8582 (tm-30) REVERT: A 298 ASN cc_start: 0.9431 (m110) cc_final: 0.8795 (m110) REVERT: A 369 LYS cc_start: 0.9609 (mtpm) cc_final: 0.9246 (mttm) REVERT: A 450 TRP cc_start: 0.9410 (t60) cc_final: 0.9147 (t60) REVERT: A 477 LYS cc_start: 0.9158 (tttt) cc_final: 0.8954 (tttt) REVERT: A 679 LYS cc_start: 0.9006 (mttp) cc_final: 0.8670 (mmtt) REVERT: A 694 ASP cc_start: 0.9437 (t0) cc_final: 0.9044 (m-30) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.2243 time to fit residues: 25.6277 Evaluate side-chains 82 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN ** A1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.078443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057652 restraints weight = 134646.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060448 restraints weight = 60526.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.062157 restraints weight = 38073.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063259 restraints weight = 28826.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.063943 restraints weight = 24202.754| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9891 Z= 0.296 Angle : 0.664 7.194 13683 Z= 0.398 Chirality : 0.042 0.304 1572 Planarity : 0.004 0.041 1458 Dihedral : 21.735 178.137 2255 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.30 % Favored : 91.39 % Rotamer: Outliers : 1.73 % Allowed : 10.73 % 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: -1.09 (0.26), residues: 952 helix: 0.20 (0.24), residues: 424 sheet: -0.26 (0.52), residues: 99 loop : -1.78 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 441 TYR 0.016 0.002 TYR A 783 PHE 0.016 0.002 PHE A1062 TRP 0.011 0.002 TRP A 897 HIS 0.006 0.002 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.30 ( 9891) covalent geometry : angle 0.66440 / 0.40 (13683) hydrogen bonds : bond 0.06219 / 4.12 ( 456) hydrogen bonds : angle 5.27982 / 3.67 ( 1172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.9619 (mtpm) cc_final: 0.9217 (mttm) REVERT: A 679 LYS cc_start: 0.9080 (mttp) cc_final: 0.8808 (mmtt) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.2385 time to fit residues: 26.1111 Evaluate side-chains 85 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.079578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058851 restraints weight = 132332.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.061691 restraints weight = 58502.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063466 restraints weight = 36535.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.064574 restraints weight = 27494.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.065165 restraints weight = 23025.636| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9891 Z= 0.170 Angle : 0.579 7.194 13683 Z= 0.349 Chirality : 0.040 0.339 1572 Planarity : 0.004 0.036 1458 Dihedral : 21.621 176.704 2255 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.46 % Favored : 92.23 % Rotamer: Outliers : 1.96 % Allowed : 11.30 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.27), residues: 952 helix: 0.60 (0.25), residues: 423 sheet: -0.11 (0.53), residues: 101 loop : -1.65 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 658 TYR 0.016 0.001 TYR A 783 PHE 0.013 0.001 PHE A 465 TRP 0.016 0.002 TRP A 450 HIS 0.005 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 ( 9891) covalent geometry : angle 0.57883 / 0.35 (13683) hydrogen bonds : bond 0.05433 / 3.58 ( 456) hydrogen bonds : angle 4.89421 / 3.39 ( 1172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.9604 (mtpm) cc_final: 0.9174 (mttm) REVERT: A 679 LYS cc_start: 0.9024 (mttp) cc_final: 0.8705 (mmtt) REVERT: A 694 ASP cc_start: 0.9455 (t0) cc_final: 0.9043 (m-30) outliers start: 17 outliers final: 15 residues processed: 83 average time/residue: 0.2236 time to fit residues: 25.4717 Evaluate side-chains 87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 0.0570 chunk 33 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 chunk 25 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.060480 restraints weight = 130006.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.063476 restraints weight = 56640.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065337 restraints weight = 34829.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.066486 restraints weight = 25898.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067232 restraints weight = 21569.892| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9891 Z= 0.118 Angle : 0.557 7.588 13683 Z= 0.329 Chirality : 0.039 0.348 1572 Planarity : 0.003 0.038 1458 Dihedral : 21.473 174.998 2255 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.51 % Favored : 93.17 % Rotamer: Outliers : 1.61 % Allowed : 11.30 % Favored : 87.08 % 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: -0.09 (0.27), residues: 952 helix: 1.11 (0.26), residues: 423 sheet: 0.38 (0.53), residues: 97 loop : -1.37 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1147 TYR 0.019 0.001 TYR A 783 PHE 0.012 0.001 PHE A 707 TRP 0.022 0.002 TRP A 450 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 9891) covalent geometry : angle 0.55698 / 0.33 (13683) hydrogen bonds : bond 0.04822 / 3.17 ( 456) hydrogen bonds : angle 4.51965 / 3.14 ( 1172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.9086 (tp40) cc_final: 0.8566 (tp-100) REVERT: A 336 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8612 (p90) REVERT: A 369 LYS cc_start: 0.9577 (mtpm) cc_final: 0.9118 (mttm) REVERT: A 409 LYS cc_start: 0.8503 (mttm) cc_final: 0.8170 (mttt) REVERT: A 679 LYS cc_start: 0.8988 (mttp) cc_final: 0.8654 (mmtt) REVERT: A 694 ASP cc_start: 0.9395 (t0) cc_final: 0.8979 (m-30) outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 0.2351 time to fit residues: 27.4484 Evaluate side-chains 88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1058 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 90 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.081151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.060827 restraints weight = 130337.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.063773 restraints weight = 57779.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.065647 restraints weight = 35489.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066838 restraints weight = 26233.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.067609 restraints weight = 21551.992| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9891 Z= 0.154 Angle : 0.543 6.965 13683 Z= 0.322 Chirality : 0.038 0.337 1572 Planarity : 0.003 0.035 1458 Dihedral : 21.474 176.335 2255 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.51 % Favored : 93.17 % Rotamer: Outliers : 1.85 % Allowed : 12.00 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.27), residues: 952 helix: 1.01 (0.25), residues: 431 sheet: 0.33 (0.52), residues: 98 loop : -1.40 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.017 0.001 TYR A 783 PHE 0.009 0.001 PHE A 465 TRP 0.020 0.002 TRP A 450 HIS 0.006 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 9891) covalent geometry : angle 0.54309 / 0.32 (13683) hydrogen bonds : bond 0.04808 / 3.17 ( 456) hydrogen bonds : angle 4.57515 / 3.18 ( 1172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.9106 (tp40) cc_final: 0.8592 (tp-100) REVERT: A 336 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8529 (p90) REVERT: A 369 LYS cc_start: 0.9586 (mtpm) cc_final: 0.9132 (mttm) REVERT: A 679 LYS cc_start: 0.9017 (mttp) cc_final: 0.8683 (mmtt) REVERT: A 694 ASP cc_start: 0.9420 (t0) cc_final: 0.8981 (m-30) outliers start: 16 outliers final: 13 residues processed: 82 average time/residue: 0.2350 time to fit residues: 26.0599 Evaluate side-chains 88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.060312 restraints weight = 131748.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063302 restraints weight = 57379.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065152 restraints weight = 35280.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066294 restraints weight = 26220.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.067019 restraints weight = 21796.204| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9891 Z= 0.114 Angle : 0.531 6.949 13683 Z= 0.313 Chirality : 0.038 0.334 1572 Planarity : 0.003 0.037 1458 Dihedral : 21.417 176.047 2255 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.72 % Favored : 92.96 % Rotamer: Outliers : 1.61 % Allowed : 12.34 % Favored : 86.04 % 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: 0.02 (0.28), residues: 952 helix: 1.16 (0.25), residues: 430 sheet: 0.46 (0.52), residues: 98 loop : -1.33 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 569 TYR 0.016 0.001 TYR A 783 PHE 0.008 0.001 PHE A 465 TRP 0.024 0.002 TRP A 450 HIS 0.005 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 9891) covalent geometry : angle 0.53085 / 0.31 (13683) hydrogen bonds : bond 0.04506 / 2.98 ( 456) hydrogen bonds : angle 4.41730 / 3.07 ( 1172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.9085 (tp40) cc_final: 0.8568 (tp-100) REVERT: A 336 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8591 (p90) REVERT: A 679 LYS cc_start: 0.9034 (mttp) cc_final: 0.8678 (mmtt) REVERT: A 694 ASP cc_start: 0.9398 (t0) cc_final: 0.8957 (m-30) outliers start: 14 outliers final: 12 residues processed: 81 average time/residue: 0.2307 time to fit residues: 25.5526 Evaluate side-chains 87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.080317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.059695 restraints weight = 131763.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.062597 restraints weight = 57871.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.064414 restraints weight = 35743.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065563 restraints weight = 26696.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066271 restraints weight = 22180.113| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9891 Z= 0.154 Angle : 0.535 6.716 13683 Z= 0.317 Chirality : 0.038 0.330 1572 Planarity : 0.003 0.034 1458 Dihedral : 21.431 177.287 2255 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.62 % Favored : 93.07 % Rotamer: Outliers : 1.73 % Allowed : 12.34 % Favored : 85.93 % 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: -0.06 (0.27), residues: 952 helix: 1.13 (0.25), residues: 430 sheet: 0.37 (0.52), residues: 98 loop : -1.39 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.016 0.001 TYR A 783 PHE 0.009 0.001 PHE A 787 TRP 0.022 0.002 TRP A 450 HIS 0.005 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 9891) covalent geometry : angle 0.53472 / 0.32 (13683) hydrogen bonds : bond 0.04583 / 3.02 ( 456) hydrogen bonds : angle 4.46472 / 3.10 ( 1172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.9103 (tp40) cc_final: 0.8590 (tp-100) REVERT: A 336 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8534 (p90) REVERT: A 679 LYS cc_start: 0.9039 (mttp) cc_final: 0.8723 (mmtt) REVERT: A 694 ASP cc_start: 0.9406 (t0) cc_final: 0.8966 (m-30) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.2392 time to fit residues: 26.3756 Evaluate side-chains 86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.080267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059733 restraints weight = 130675.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.062640 restraints weight = 57293.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064428 restraints weight = 35314.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065568 restraints weight = 26523.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066249 restraints weight = 21951.598| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.281 9891 Z= 0.240 Angle : 0.829 59.183 13683 Z= 0.511 Chirality : 0.043 0.830 1572 Planarity : 0.004 0.056 1458 Dihedral : 21.432 177.262 2255 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.62 % Favored : 93.07 % Rotamer: Outliers : 1.61 % Allowed : 12.23 % Favored : 86.16 % Cbeta Deviations : 0.11 % 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: -0.07 (0.27), residues: 952 helix: 1.12 (0.25), residues: 430 sheet: 0.37 (0.52), residues: 98 loop : -1.40 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.016 0.001 TYR A 783 PHE 0.036 0.001 PHE A 247 TRP 0.019 0.002 TRP A 450 HIS 0.005 0.001 HIS A1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.24 ( 9891) covalent geometry : angle 0.82911 / 0.51 (13683) hydrogen bonds : bond 0.04588 / 3.03 ( 456) hydrogen bonds : angle 4.46201 / 3.10 ( 1172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.49 seconds wall clock time: 51 minutes 59.73 seconds (3119.73 seconds total)