Starting phenix.real_space_refine on Thu Sep 18 00:57:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl7_45664/09_2025/9cl7_45664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl7_45664/09_2025/9cl7_45664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cl7_45664/09_2025/9cl7_45664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl7_45664/09_2025/9cl7_45664.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cl7_45664/09_2025/9cl7_45664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl7_45664/09_2025/9cl7_45664.map" } resolution = 3.83 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= 0.015 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: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 75 5.16 5 C 7742 2.51 5 N 2187 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12714 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 949 Classifications: {'DNA': 46} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 817 Classifications: {'DNA': 40} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 39} Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "E" Number of atoms: 4924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4924 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 4 Time building chain proxies: 3.37, per 1000 atoms: 0.27 Number of scatterers: 12714 At special positions: 0 Unit cell: (102.03, 111.696, 147.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 86 15.00 O 2624 8.00 N 2187 7.00 C 7742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 162 " distance=2.03 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: 1.19 Conformation dependent library (CDL) restraints added in 565.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 41.4% alpha, 18.2% beta 29 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.972A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.603A pdb=" N CYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.913A pdb=" N HIS B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'C' and resid 8 through 21 removed outlier: 4.041A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 removed outlier: 3.795A pdb=" N CYS C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.825A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 222 Proline residue: C 220 - end of helix No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.749A pdb=" N GLY C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 261 " --> pdb=" O ASP C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'D' and resid 8 through 20 removed outlier: 4.213A pdb=" N LEU D 12 " --> pdb=" O GLN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 141 through 152 Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 217 through 222 Proline residue: D 220 - end of helix No H-bonds generated for 'chain 'D' and resid 217 through 222' Processing helix chain 'E' and resid 373 through 389 Processing helix chain 'E' and resid 390 through 394 removed outlier: 3.545A pdb=" N MET E 393 " --> pdb=" O GLU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 410 removed outlier: 3.590A pdb=" N LYS E 401 " --> pdb=" O ASP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 424 removed outlier: 3.580A pdb=" N ARG E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'E' and resid 443 through 453 Processing helix chain 'E' and resid 460 through 462 No H-bonds generated for 'chain 'E' and resid 460 through 462' Processing helix chain 'E' and resid 464 through 472 removed outlier: 3.528A pdb=" N VAL E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 485 Processing helix chain 'E' and resid 492 through 506 removed outlier: 3.587A pdb=" N LYS E 505 " --> pdb=" O LEU E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 513 Processing helix chain 'E' and resid 518 through 532 removed outlier: 3.982A pdb=" N VAL E 522 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 548 removed outlier: 3.818A pdb=" N ILE E 548 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 554 removed outlier: 3.680A pdb=" N PHE E 552 " --> pdb=" O ILE E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 582 Processing helix chain 'E' and resid 598 through 622 removed outlier: 3.730A pdb=" N LEU E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 641 removed outlier: 3.795A pdb=" N ALA E 627 " --> pdb=" O ASN E 623 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU E 629 " --> pdb=" O GLU E 625 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 653 removed outlier: 3.886A pdb=" N ARG E 648 " --> pdb=" O HIS E 644 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS E 649 " --> pdb=" O PRO E 645 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS E 650 " --> pdb=" O SER E 646 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU E 651 " --> pdb=" O LEU E 647 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP E 652 " --> pdb=" O ARG E 648 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU E 653 " --> pdb=" O CYS E 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 644 through 653' Processing helix chain 'E' and resid 654 through 659 Processing helix chain 'E' and resid 661 through 680 removed outlier: 3.629A pdb=" N GLU E 675 " --> pdb=" O SER E 671 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 680 " --> pdb=" O ILE E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 695 removed outlier: 4.018A pdb=" N SER E 695 " --> pdb=" O GLU E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 718 removed outlier: 4.030A pdb=" N TRP E 708 " --> pdb=" O ARG E 704 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP E 709 " --> pdb=" O GLY E 705 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS E 718 " --> pdb=" O ASN E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 733 Processing helix chain 'E' and resid 740 through 756 removed outlier: 4.167A pdb=" N LEU E 746 " --> pdb=" O HIS E 742 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 748 " --> pdb=" O LEU E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 825 removed outlier: 4.279A pdb=" N LEU E 817 " --> pdb=" O SER E 813 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 818 " --> pdb=" O VAL E 814 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N HIS E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 846 removed outlier: 3.698A pdb=" N LEU E 844 " --> pdb=" O THR E 840 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 845 " --> pdb=" O LEU E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 852 Processing helix chain 'E' and resid 872 through 879 removed outlier: 4.288A pdb=" N PHE E 876 " --> pdb=" O THR E 872 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG E 879 " --> pdb=" O PHE E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 893 Processing helix chain 'E' and resid 894 through 909 Processing helix chain 'E' and resid 918 through 922 Processing helix chain 'E' and resid 924 through 935 Processing helix chain 'E' and resid 937 through 948 removed outlier: 4.336A pdb=" N SER E 941 " --> pdb=" O GLY E 937 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL E 943 " --> pdb=" O VAL E 939 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS E 946 " --> pdb=" O GLY E 942 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA E 948 " --> pdb=" O CYS E 944 " (cutoff:3.500A) Processing helix chain 'E' and resid 984 through 996 removed outlier: 3.579A pdb=" N MET E 988 " --> pdb=" O SER E 984 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 989 " --> pdb=" O HIS E 985 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.602A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 61 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 104 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.602A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 61 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 101 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 29 Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 40 removed outlier: 4.360A pdb=" N HIS B 246 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 197 through 198 removed outlier: 3.680A pdb=" N VAL B 136 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AA7, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.515A pdb=" N PHE B 207 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 170 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 182 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN B 177 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 115 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 91 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR D 59 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.515A pdb=" N PHE B 207 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 170 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 182 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 111 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 62 removed outlier: 3.643A pdb=" N ARG C 61 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL C 102 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 99 " --> pdb=" O MET C 116 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET C 116 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL C 111 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 181 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 182 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 167 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.580A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 48 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 49 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS C 246 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AB3, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.624A pdb=" N MET D 68 " --> pdb=" O TRP D 28 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N CYS D 27 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS D 246 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 136 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 429 through 430 removed outlier: 3.606A pdb=" N VAL E 535 " --> pdb=" O ILE E 429 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 975 through 977 removed outlier: 7.257A pdb=" N GLU E 975 " --> pdb=" O CYS E1004 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 486 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3844 1.34 - 1.46: 2626 1.46 - 1.58: 6353 1.58 - 1.70: 170 1.70 - 1.82: 116 Bond restraints: 13109 Sorted by residual: bond pdb=" CG LEU E 472 " pdb=" CD2 LEU E 472 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" C MET C 68 " pdb=" N GLY C 69 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 2.00e+00 bond pdb=" CB MET E 558 " pdb=" CG MET E 558 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CA VAL C 233 " pdb=" C VAL C 233 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.23e+00 bond pdb=" CB MET E 772 " pdb=" CG MET E 772 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 ... (remaining 13104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 17959 3.13 - 6.25: 103 6.25 - 9.38: 19 9.38 - 12.51: 6 12.51 - 15.64: 2 Bond angle restraints: 18089 Sorted by residual: angle pdb=" CB MET E 558 " pdb=" CG MET E 558 " pdb=" SD MET E 558 " ideal model delta sigma weight residual 112.70 128.34 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" CA MET E 772 " pdb=" CB MET E 772 " pdb=" CG MET E 772 " ideal model delta sigma weight residual 114.10 122.63 -8.53 2.00e+00 2.50e-01 1.82e+01 angle pdb=" CA LEU E 524 " pdb=" CB LEU E 524 " pdb=" CG LEU E 524 " ideal model delta sigma weight residual 116.30 130.62 -14.32 3.50e+00 8.16e-02 1.68e+01 angle pdb=" CB MET C 116 " pdb=" CG MET C 116 " pdb=" SD MET C 116 " ideal model delta sigma weight residual 112.70 124.01 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CB MET D 244 " pdb=" CG MET D 244 " pdb=" SD MET D 244 " ideal model delta sigma weight residual 112.70 123.59 -10.89 3.00e+00 1.11e-01 1.32e+01 ... (remaining 18084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 6067 18.00 - 35.99: 1063 35.99 - 53.99: 494 53.99 - 71.99: 111 71.99 - 89.98: 23 Dihedral angle restraints: 7758 sinusoidal: 3695 harmonic: 4063 Sorted by residual: dihedral pdb=" CA SER B 161 " pdb=" C SER B 161 " pdb=" N CYS B 162 " pdb=" CA CYS B 162 " ideal model delta harmonic sigma weight residual -180.00 -154.33 -25.67 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA GLU E 476 " pdb=" C GLU E 476 " pdb=" N LEU E 477 " pdb=" CA LEU E 477 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 162 " pdb=" CB CYS B 162 " ideal model delta sinusoidal sigma weight residual -86.00 -117.47 31.47 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 7755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1463 0.038 - 0.075: 446 0.075 - 0.113: 144 0.113 - 0.150: 16 0.150 - 0.188: 2 Chirality restraints: 2071 Sorted by residual: chirality pdb=" CB VAL E 544 " pdb=" CA VAL E 544 " pdb=" CG1 VAL E 544 " pdb=" CG2 VAL E 544 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA GLU E 476 " pdb=" N GLU E 476 " pdb=" C GLU E 476 " pdb=" CB GLU E 476 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CG LEU E 477 " pdb=" CB LEU E 477 " pdb=" CD1 LEU E 477 " pdb=" CD2 LEU E 477 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 2068 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 215 " 0.020 2.00e-02 2.50e+03 1.66e-02 4.81e+00 pdb=" CG PHE B 215 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 215 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 215 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 215 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 215 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 215 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 233 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 234 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C THR C 89 " 0.028 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 90 " -0.009 2.00e-02 2.50e+03 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 795 2.72 - 3.26: 13465 3.26 - 3.81: 22828 3.81 - 4.35: 26329 4.35 - 4.90: 40479 Nonbonded interactions: 103896 Sorted by model distance: nonbonded pdb=" O ARG E 721 " pdb=" OG1 THR E 725 " model vdw 2.174 3.040 nonbonded pdb=" O SER C 31 " pdb=" OH TYR C 60 " model vdw 2.186 3.040 nonbonded pdb=" O LEU E 550 " pdb=" OG SER E 553 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP D 41 " pdb=" OG SER D 43 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP B 41 " pdb=" OH TYR B 211 " model vdw 2.216 3.040 ... (remaining 103891 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 0.053 13112 Z= 0.149 Angle : 0.703 15.635 18095 Z= 0.351 Chirality : 0.040 0.188 2071 Planarity : 0.003 0.051 2018 Dihedral : 21.866 89.983 5107 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 0.25 % Allowed : 35.19 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.23), residues: 1379 helix: 0.56 (0.25), residues: 440 sheet: -0.80 (0.28), residues: 363 loop : -1.20 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 542 TYR 0.011 0.001 TYR D 249 PHE 0.037 0.002 PHE B 215 TRP 0.011 0.001 TRP E 708 HIS 0.003 0.001 HIS E 650 Details of bonding type rmsd covalent geometry : bond 0.00316 (13109) covalent geometry : angle 0.70265 (18089) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.82350 ( 6) hydrogen bonds : bond 0.24494 ( 539) hydrogen bonds : angle 8.85765 ( 1462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 MET cc_start: 0.6875 (tpt) cc_final: 0.6624 (tpt) REVERT: E 848 ASP cc_start: 0.9715 (m-30) cc_final: 0.9434 (p0) outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.1058 time to fit residues: 13.9193 Evaluate side-chains 79 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** E 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 891 HIS ** E 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.089931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.060361 restraints weight = 82327.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.061791 restraints weight = 44127.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.062816 restraints weight = 30055.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.063636 restraints weight = 23910.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.063890 restraints weight = 20623.949| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13112 Z= 0.168 Angle : 0.650 9.993 18095 Z= 0.343 Chirality : 0.042 0.199 2071 Planarity : 0.004 0.051 2018 Dihedral : 21.793 81.047 2438 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 3.77 % Allowed : 31.17 % Favored : 65.05 % 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 aren not related in a simple way. whole: -0.75 (0.23), residues: 1379 helix: 0.69 (0.24), residues: 456 sheet: -0.73 (0.29), residues: 350 loop : -1.23 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 61 TYR 0.027 0.002 TYR E 842 PHE 0.030 0.001 PHE B 215 TRP 0.013 0.001 TRP C 28 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00356 (13109) covalent geometry : angle 0.65010 (18089) SS BOND : bond 0.00321 ( 3) SS BOND : angle 0.76074 ( 6) hydrogen bonds : bond 0.07005 ( 539) hydrogen bonds : angle 5.95730 ( 1462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 78 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9443 (tmm) cc_final: 0.9190 (tmm) REVERT: B 199 MET cc_start: 0.6740 (tpt) cc_final: 0.6515 (tpt) REVERT: B 244 MET cc_start: 0.8470 (tmm) cc_final: 0.8195 (tmm) REVERT: C 1 MET cc_start: 0.7770 (tpp) cc_final: 0.7380 (tpp) REVERT: C 116 MET cc_start: 0.8490 (ppp) cc_final: 0.7353 (ppp) REVERT: C 119 MET cc_start: 0.8627 (tmm) cc_final: 0.7983 (tmm) REVERT: D 40 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8027 (tmm) REVERT: E 848 ASP cc_start: 0.9749 (m-30) cc_final: 0.9427 (p0) outliers start: 46 outliers final: 21 residues processed: 118 average time/residue: 0.1047 time to fit residues: 19.1063 Evaluate side-chains 97 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 612 LEU Chi-restraints excluded: chain E residue 814 VAL Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 101 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 909 GLN ** 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 = 0.4079 r_free = 0.4079 target = 0.091258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.064185 restraints weight = 82683.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.064157 restraints weight = 46194.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.064339 restraints weight = 33993.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064384 restraints weight = 30847.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064448 restraints weight = 28083.715| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13112 Z= 0.123 Angle : 0.623 11.271 18095 Z= 0.322 Chirality : 0.041 0.157 2071 Planarity : 0.004 0.047 2018 Dihedral : 21.667 78.275 2436 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.58 % Favored : 94.34 % Rotamer: Outliers : 3.20 % Allowed : 30.02 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.23), residues: 1379 helix: 0.88 (0.25), residues: 449 sheet: -0.67 (0.30), residues: 334 loop : -1.26 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 64 TYR 0.021 0.001 TYR E 842 PHE 0.026 0.001 PHE B 215 TRP 0.012 0.001 TRP E 638 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00255 (13109) covalent geometry : angle 0.62272 (18089) SS BOND : bond 0.00530 ( 3) SS BOND : angle 0.86969 ( 6) hydrogen bonds : bond 0.06369 ( 539) hydrogen bonds : angle 5.41667 ( 1462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.9159 (tmm) REVERT: B 244 MET cc_start: 0.8423 (tmm) cc_final: 0.8200 (tmm) REVERT: C 1 MET cc_start: 0.7926 (tpp) cc_final: 0.7721 (tpp) REVERT: C 79 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9422 (tt) REVERT: C 116 MET cc_start: 0.8420 (ppp) cc_final: 0.7422 (ppp) REVERT: C 119 MET cc_start: 0.8615 (tmm) cc_final: 0.8096 (tmm) REVERT: D 1 MET cc_start: 0.8577 (tpt) cc_final: 0.8325 (tpp) REVERT: D 40 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7995 (tmm) REVERT: D 99 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9016 (pp) REVERT: E 848 ASP cc_start: 0.9713 (m-30) cc_final: 0.9319 (p0) outliers start: 39 outliers final: 16 residues processed: 115 average time/residue: 0.0999 time to fit residues: 18.1661 Evaluate side-chains 96 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 814 VAL Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN D 8 GLN D 44 HIS E 457 GLN E 492 GLN ** E 909 GLN ** 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 = 0.4021 r_free = 0.4021 target = 0.087623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.060222 restraints weight = 83911.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.060257 restraints weight = 45539.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060398 restraints weight = 33547.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060429 restraints weight = 31690.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060503 restraints weight = 28912.264| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13112 Z= 0.227 Angle : 0.663 13.414 18095 Z= 0.345 Chirality : 0.041 0.166 2071 Planarity : 0.004 0.044 2018 Dihedral : 21.862 75.560 2436 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.18 % Rotamer: Outliers : 5.00 % Allowed : 29.20 % Favored : 65.79 % 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 aren not related in a simple way. whole: -0.79 (0.23), residues: 1379 helix: 0.74 (0.24), residues: 451 sheet: -1.00 (0.27), residues: 375 loop : -1.11 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 149 TYR 0.023 0.002 TYR D 249 PHE 0.034 0.002 PHE B 215 TRP 0.010 0.001 TRP C 28 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00483 (13109) covalent geometry : angle 0.66254 (18089) SS BOND : bond 0.00390 ( 3) SS BOND : angle 0.74677 ( 6) hydrogen bonds : bond 0.06857 ( 539) hydrogen bonds : angle 5.46236 ( 1462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 75 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9545 (tmm) cc_final: 0.9222 (tmm) REVERT: B 154 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9190 (tp) REVERT: B 229 MET cc_start: 0.7990 (ppp) cc_final: 0.7333 (ppp) REVERT: C 54 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.8852 (m) REVERT: C 119 MET cc_start: 0.8636 (tmm) cc_final: 0.8163 (tmm) REVERT: C 229 MET cc_start: 0.8769 (pmt) cc_final: 0.8482 (pmt) REVERT: D 40 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8048 (tmm) REVERT: D 99 LEU cc_start: 0.9450 (tp) cc_final: 0.9182 (pp) REVERT: D 207 PHE cc_start: 0.8707 (m-80) cc_final: 0.8312 (m-80) REVERT: E 848 ASP cc_start: 0.9751 (m-30) cc_final: 0.9337 (p0) outliers start: 61 outliers final: 39 residues processed: 129 average time/residue: 0.1038 time to fit residues: 21.0032 Evaluate side-chains 115 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 73 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 612 LEU Chi-restraints excluded: chain E residue 624 TRP Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 814 VAL Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 931 LEU Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 984 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 20 optimal weight: 0.0000 chunk 131 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 10 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** 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 = 0.4069 r_free = 0.4069 target = 0.090238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.060408 restraints weight = 82781.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.062110 restraints weight = 43746.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.063160 restraints weight = 29322.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.063998 restraints weight = 23546.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.064227 restraints weight = 20167.751| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13112 Z= 0.122 Angle : 0.644 14.972 18095 Z= 0.326 Chirality : 0.041 0.163 2071 Planarity : 0.003 0.043 2018 Dihedral : 21.808 74.591 2436 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 3.36 % Allowed : 30.93 % Favored : 65.71 % 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 aren not related in a simple way. whole: -0.70 (0.23), residues: 1379 helix: 0.81 (0.24), residues: 458 sheet: -0.86 (0.28), residues: 353 loop : -1.17 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 704 TYR 0.021 0.001 TYR E 842 PHE 0.030 0.001 PHE B 215 TRP 0.011 0.001 TRP E 638 HIS 0.003 0.001 HIS E 650 Details of bonding type rmsd covalent geometry : bond 0.00255 (13109) covalent geometry : angle 0.64358 (18089) SS BOND : bond 0.00450 ( 3) SS BOND : angle 1.41038 ( 6) hydrogen bonds : bond 0.05673 ( 539) hydrogen bonds : angle 5.11804 ( 1462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8057 (tmm) cc_final: 0.7797 (tmm) REVERT: B 72 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8924 (mm) REVERT: B 139 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9179 (tmm) REVERT: B 229 MET cc_start: 0.8078 (ppp) cc_final: 0.7346 (ppp) REVERT: C 54 SER cc_start: 0.9408 (OUTLIER) cc_final: 0.8797 (m) REVERT: C 79 LEU cc_start: 0.9715 (tp) cc_final: 0.9469 (tt) REVERT: C 119 MET cc_start: 0.8551 (tmm) cc_final: 0.8196 (tmm) REVERT: C 199 MET cc_start: 0.8030 (tpp) cc_final: 0.7610 (tpp) REVERT: C 213 ASN cc_start: 0.9552 (OUTLIER) cc_final: 0.9183 (m-40) REVERT: C 229 MET cc_start: 0.8899 (pmt) cc_final: 0.8680 (pmt) REVERT: D 1 MET cc_start: 0.8787 (tpp) cc_final: 0.8137 (tpp) REVERT: D 40 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7918 (tmm) REVERT: D 99 LEU cc_start: 0.9427 (tp) cc_final: 0.9167 (pp) REVERT: D 207 PHE cc_start: 0.8713 (m-80) cc_final: 0.8373 (m-80) REVERT: E 472 LEU cc_start: 0.9521 (tt) cc_final: 0.9310 (pp) REVERT: E 477 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9376 (mm) REVERT: E 848 ASP cc_start: 0.9748 (m-30) cc_final: 0.9450 (p0) outliers start: 41 outliers final: 25 residues processed: 118 average time/residue: 0.1100 time to fit residues: 19.9639 Evaluate side-chains 106 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 10.0000 chunk 85 optimal weight: 0.0470 chunk 35 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 0.0060 chunk 146 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.9898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN ** D 131 GLN ** 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 = 0.4045 r_free = 0.4045 target = 0.088854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.058876 restraints weight = 82805.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.060544 restraints weight = 43875.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.061561 restraints weight = 30114.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062421 restraints weight = 24206.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062425 restraints weight = 20902.408| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13112 Z= 0.152 Angle : 0.635 12.228 18095 Z= 0.325 Chirality : 0.040 0.165 2071 Planarity : 0.004 0.042 2018 Dihedral : 21.708 74.054 2436 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 4.59 % Allowed : 30.11 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.23), residues: 1379 helix: 0.91 (0.24), residues: 457 sheet: -0.82 (0.27), residues: 367 loop : -1.16 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 710 TYR 0.020 0.002 TYR E 842 PHE 0.030 0.001 PHE B 215 TRP 0.009 0.001 TRP E 847 HIS 0.005 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00327 (13109) covalent geometry : angle 0.63429 (18089) SS BOND : bond 0.00050 ( 3) SS BOND : angle 1.82941 ( 6) hydrogen bonds : bond 0.05776 ( 539) hydrogen bonds : angle 5.09176 ( 1462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 79 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8910 (mm) REVERT: B 112 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8677 (p) REVERT: B 139 MET cc_start: 0.9533 (OUTLIER) cc_final: 0.9229 (tmm) REVERT: B 229 MET cc_start: 0.7822 (ppp) cc_final: 0.7031 (ppp) REVERT: C 1 MET cc_start: 0.8212 (tpp) cc_final: 0.7612 (tpp) REVERT: C 54 SER cc_start: 0.9455 (OUTLIER) cc_final: 0.8827 (m) REVERT: C 119 MET cc_start: 0.8583 (tmm) cc_final: 0.8235 (tmm) REVERT: C 199 MET cc_start: 0.8005 (tpp) cc_final: 0.7707 (tpp) REVERT: C 229 MET cc_start: 0.8863 (pmt) cc_final: 0.8599 (pmt) REVERT: D 1 MET cc_start: 0.8841 (tpp) cc_final: 0.8190 (tpp) REVERT: D 40 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7959 (tmm) REVERT: D 99 LEU cc_start: 0.9430 (tp) cc_final: 0.9184 (pp) REVERT: D 207 PHE cc_start: 0.8727 (m-80) cc_final: 0.8374 (m-80) REVERT: E 468 VAL cc_start: 0.9845 (OUTLIER) cc_final: 0.9581 (p) REVERT: E 472 LEU cc_start: 0.9539 (tt) cc_final: 0.9328 (pp) REVERT: E 477 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9406 (mm) REVERT: E 848 ASP cc_start: 0.9776 (m-30) cc_final: 0.9499 (p0) outliers start: 56 outliers final: 36 residues processed: 130 average time/residue: 0.0982 time to fit residues: 19.9494 Evaluate side-chains 118 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 75 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 624 TRP Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 8 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 909 GLN ** 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 = 0.3991 r_free = 0.3991 target = 0.085608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.055882 restraints weight = 85019.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.057456 restraints weight = 45526.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.058258 restraints weight = 30881.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.059127 restraints weight = 24747.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.059327 restraints weight = 21878.993| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13112 Z= 0.268 Angle : 0.715 13.850 18095 Z= 0.367 Chirality : 0.042 0.162 2071 Planarity : 0.004 0.042 2018 Dihedral : 22.087 74.964 2436 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.18 % Rotamer: Outliers : 5.33 % Allowed : 29.70 % Favored : 64.97 % 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 aren not related in a simple way. whole: -0.90 (0.23), residues: 1379 helix: 0.65 (0.24), residues: 450 sheet: -1.01 (0.27), residues: 355 loop : -1.23 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 721 TYR 0.030 0.002 TYR D 249 PHE 0.040 0.002 PHE B 215 TRP 0.011 0.001 TRP E 847 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00567 (13109) covalent geometry : angle 0.71482 (18089) SS BOND : bond 0.00582 ( 3) SS BOND : angle 1.45392 ( 6) hydrogen bonds : bond 0.06811 ( 539) hydrogen bonds : angle 5.49629 ( 1462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 73 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8924 (mm) REVERT: B 116 MET cc_start: 0.9142 (tpp) cc_final: 0.8881 (tpt) REVERT: B 139 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.9123 (ppp) REVERT: B 229 MET cc_start: 0.7871 (ppp) cc_final: 0.7048 (ppp) REVERT: C 1 MET cc_start: 0.8091 (tpp) cc_final: 0.7558 (tpp) REVERT: C 54 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.8801 (m) REVERT: C 79 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9509 (tt) REVERT: C 119 MET cc_start: 0.8566 (tmm) cc_final: 0.8205 (tmm) REVERT: C 229 MET cc_start: 0.8779 (pmt) cc_final: 0.8515 (pmt) REVERT: D 40 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8037 (tmm) REVERT: D 99 LEU cc_start: 0.9495 (tp) cc_final: 0.9264 (pp) REVERT: E 848 ASP cc_start: 0.9792 (m-30) cc_final: 0.9538 (p0) outliers start: 65 outliers final: 50 residues processed: 131 average time/residue: 0.1028 time to fit residues: 20.8743 Evaluate side-chains 125 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 70 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 612 LEU Chi-restraints excluded: chain E residue 624 TRP Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 708 TRP Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 931 LEU Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 964 TRP Chi-restraints excluded: chain E residue 984 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 0.0070 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** 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 = 0.4041 r_free = 0.4041 target = 0.088408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.058665 restraints weight = 82187.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.060260 restraints weight = 43404.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.061506 restraints weight = 29918.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062293 restraints weight = 24076.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.062790 restraints weight = 20912.964| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13112 Z= 0.124 Angle : 0.671 13.290 18095 Z= 0.334 Chirality : 0.041 0.223 2071 Planarity : 0.003 0.043 2018 Dihedral : 21.927 74.351 2436 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 3.94 % Allowed : 31.09 % Favored : 64.97 % 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 aren not related in a simple way. whole: -0.65 (0.23), residues: 1379 helix: 0.96 (0.25), residues: 448 sheet: -0.92 (0.27), residues: 371 loop : -1.13 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 710 TYR 0.019 0.001 TYR E 842 PHE 0.033 0.002 PHE B 215 TRP 0.013 0.001 TRP C 28 HIS 0.003 0.001 HIS E 650 Details of bonding type rmsd covalent geometry : bond 0.00265 (13109) covalent geometry : angle 0.67060 (18089) SS BOND : bond 0.00401 ( 3) SS BOND : angle 1.45863 ( 6) hydrogen bonds : bond 0.05452 ( 539) hydrogen bonds : angle 5.06056 ( 1462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 77 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8973 (mm) REVERT: B 139 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.9194 (tmm) REVERT: B 229 MET cc_start: 0.7890 (ppp) cc_final: 0.7031 (ppp) REVERT: C 1 MET cc_start: 0.8239 (tpp) cc_final: 0.7740 (tpp) REVERT: C 54 SER cc_start: 0.9455 (OUTLIER) cc_final: 0.8813 (m) REVERT: C 119 MET cc_start: 0.8600 (tmm) cc_final: 0.8283 (tmm) REVERT: C 199 MET cc_start: 0.7957 (tpp) cc_final: 0.7621 (tpp) REVERT: D 1 MET cc_start: 0.9018 (tpp) cc_final: 0.8332 (tpp) REVERT: D 40 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7910 (tmm) REVERT: D 99 LEU cc_start: 0.9428 (tp) cc_final: 0.9210 (pp) REVERT: D 207 PHE cc_start: 0.8718 (m-80) cc_final: 0.8430 (m-80) REVERT: E 848 ASP cc_start: 0.9768 (m-30) cc_final: 0.9514 (p0) outliers start: 48 outliers final: 36 residues processed: 119 average time/residue: 0.0999 time to fit residues: 18.6593 Evaluate side-chains 114 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 74 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 624 TRP Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 964 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 61 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 137 optimal weight: 0.0060 chunk 55 optimal weight: 0.0980 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 GLN ** 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 = 0.4022 r_free = 0.4022 target = 0.087134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.057444 restraints weight = 83386.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.059071 restraints weight = 44125.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060255 restraints weight = 30374.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.061047 restraints weight = 23694.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.061183 restraints weight = 20540.928| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13112 Z= 0.162 Angle : 0.670 14.471 18095 Z= 0.334 Chirality : 0.040 0.153 2071 Planarity : 0.004 0.043 2018 Dihedral : 21.881 74.134 2436 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.43 % Allowed : 30.60 % Favored : 64.97 % 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 aren not related in a simple way. whole: -0.62 (0.23), residues: 1379 helix: 0.97 (0.25), residues: 449 sheet: -0.88 (0.27), residues: 371 loop : -1.13 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 710 TYR 0.020 0.002 TYR E 842 PHE 0.034 0.002 PHE B 215 TRP 0.012 0.001 TRP E 847 HIS 0.002 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00350 (13109) covalent geometry : angle 0.66953 (18089) SS BOND : bond 0.00322 ( 3) SS BOND : angle 1.21651 ( 6) hydrogen bonds : bond 0.05704 ( 539) hydrogen bonds : angle 5.10510 ( 1462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 75 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8947 (mm) REVERT: B 112 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 139 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.9126 (ppp) REVERT: B 229 MET cc_start: 0.7895 (ppp) cc_final: 0.7038 (ppp) REVERT: C 1 MET cc_start: 0.8281 (tpp) cc_final: 0.7933 (tpp) REVERT: C 54 SER cc_start: 0.9449 (OUTLIER) cc_final: 0.8811 (m) REVERT: C 119 MET cc_start: 0.8540 (tmm) cc_final: 0.8248 (tmm) REVERT: C 126 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8826 (mp) REVERT: D 1 MET cc_start: 0.9092 (tpp) cc_final: 0.8435 (tpp) REVERT: D 40 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7938 (tmm) REVERT: D 207 PHE cc_start: 0.8672 (m-80) cc_final: 0.8395 (m-80) REVERT: E 461 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8717 (pm20) REVERT: E 848 ASP cc_start: 0.9778 (m-30) cc_final: 0.9540 (p0) outliers start: 54 outliers final: 42 residues processed: 124 average time/residue: 0.0973 time to fit residues: 19.1013 Evaluate side-chains 123 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 74 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 624 TRP Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 964 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.0020 chunk 144 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 GLN ** 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 = 0.4035 r_free = 0.4035 target = 0.087776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.058082 restraints weight = 83178.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.059807 restraints weight = 43774.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.060987 restraints weight = 30033.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.061840 restraints weight = 23591.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.062169 restraints weight = 20430.947| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13112 Z= 0.134 Angle : 0.682 15.329 18095 Z= 0.335 Chirality : 0.041 0.162 2071 Planarity : 0.003 0.043 2018 Dihedral : 21.841 74.037 2436 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.77 % Allowed : 31.34 % Favored : 64.89 % 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 aren not related in a simple way. whole: -0.60 (0.23), residues: 1379 helix: 1.00 (0.25), residues: 449 sheet: -0.84 (0.27), residues: 367 loop : -1.15 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 710 TYR 0.019 0.001 TYR E 842 PHE 0.032 0.001 PHE B 215 TRP 0.011 0.001 TRP E 847 HIS 0.002 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00289 (13109) covalent geometry : angle 0.68187 (18089) SS BOND : bond 0.00334 ( 3) SS BOND : angle 1.26419 ( 6) hydrogen bonds : bond 0.05363 ( 539) hydrogen bonds : angle 4.97561 ( 1462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8969 (mm) REVERT: B 112 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8824 (p) REVERT: B 139 MET cc_start: 0.9521 (OUTLIER) cc_final: 0.9189 (tmm) REVERT: B 229 MET cc_start: 0.7908 (ppp) cc_final: 0.7045 (ppp) REVERT: C 1 MET cc_start: 0.8294 (tpp) cc_final: 0.7930 (tpp) REVERT: C 54 SER cc_start: 0.9447 (OUTLIER) cc_final: 0.8795 (m) REVERT: C 119 MET cc_start: 0.8589 (tmm) cc_final: 0.8292 (tmm) REVERT: C 126 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8826 (mp) REVERT: D 1 MET cc_start: 0.9084 (tpp) cc_final: 0.8379 (tpp) REVERT: D 40 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8038 (tmm) REVERT: D 207 PHE cc_start: 0.8741 (m-80) cc_final: 0.8491 (m-80) REVERT: E 461 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8758 (pm20) REVERT: E 848 ASP cc_start: 0.9779 (m-30) cc_final: 0.9545 (p0) outliers start: 46 outliers final: 35 residues processed: 118 average time/residue: 0.0982 time to fit residues: 18.4951 Evaluate side-chains 117 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 75 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 624 TRP Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 964 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 111 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 96 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 70 optimal weight: 0.0370 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 GLN ** 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 = 0.4053 r_free = 0.4053 target = 0.088715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.059223 restraints weight = 82397.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.060949 restraints weight = 43185.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.061757 restraints weight = 29105.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.062741 restraints weight = 23554.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063025 restraints weight = 20170.565| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13112 Z= 0.119 Angle : 0.683 14.346 18095 Z= 0.332 Chirality : 0.041 0.175 2071 Planarity : 0.003 0.044 2018 Dihedral : 21.708 77.661 2436 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.69 % Allowed : 31.67 % Favored : 64.64 % 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 aren not related in a simple way. whole: -0.52 (0.23), residues: 1379 helix: 1.07 (0.25), residues: 452 sheet: -0.67 (0.29), residues: 342 loop : -1.22 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 710 TYR 0.018 0.001 TYR E 842 PHE 0.029 0.001 PHE B 215 TRP 0.011 0.001 TRP E 847 HIS 0.002 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00257 (13109) covalent geometry : angle 0.68248 (18089) SS BOND : bond 0.00378 ( 3) SS BOND : angle 0.87385 ( 6) hydrogen bonds : bond 0.05306 ( 539) hydrogen bonds : angle 4.82763 ( 1462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3314.81 seconds wall clock time: 57 minutes 54.38 seconds (3474.38 seconds total)