Starting phenix.real_space_refine on Thu May 15 05:20:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl7_45664/05_2025/9cl7_45664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl7_45664/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cl7_45664/05_2025/9cl7_45664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl7_45664/05_2025/9cl7_45664.map" model { file = "/net/cci-nas-00/data/ceres_data/9cl7_45664/05_2025/9cl7_45664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl7_45664/05_2025/9cl7_45664.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.82, per 1000 atoms: 0.62 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.68 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: 5.57 Time building geometry restraints manager: 3.78 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: 0.850 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.940 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- 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 : 21.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP E 708 HIS 0.003 0.001 HIS E 650 PHE 0.037 0.002 PHE B 215 TYR 0.011 0.001 TYR D 249 ARG 0.008 0.000 ARG E 542 Details of bonding type rmsd hydrogen bonds : bond 0.24494 ( 539) hydrogen bonds : angle 8.85765 ( 1462) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.82350 ( 6) covalent geometry : bond 0.00316 (13109) covalent geometry : angle 0.70265 (18089) *********************** 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 : 1.356 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: 0.2195 time to fit residues: 28.7324 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 : 1.227 ------------------------------------------------------------------------------- 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 124 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN 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 = 0.4049 r_free = 0.4049 target = 0.089332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.059521 restraints weight = 82733.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061147 restraints weight = 44678.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.062212 restraints weight = 30197.458| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13112 Z= 0.191 Angle : 0.657 10.436 18095 Z= 0.347 Chirality : 0.041 0.196 2071 Planarity : 0.004 0.051 2018 Dihedral : 21.788 80.942 2438 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.18 % Rotamer: Outliers : 3.53 % Allowed : 31.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1379 helix: 0.60 (0.24), residues: 462 sheet: -0.61 (0.30), residues: 340 loop : -1.27 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 28 HIS 0.003 0.001 HIS E 594 PHE 0.030 0.002 PHE B 215 TYR 0.024 0.002 TYR E 842 ARG 0.004 0.000 ARG E 982 Details of bonding type rmsd hydrogen bonds : bond 0.07722 ( 539) hydrogen bonds : angle 6.20707 ( 1462) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.73323 ( 6) covalent geometry : bond 0.00401 (13109) covalent geometry : angle 0.65721 (18089) *********************** 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 120 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9429 (tmm) cc_final: 0.9165 (tmm) REVERT: B 199 MET cc_start: 0.6788 (tpt) cc_final: 0.6489 (tpt) REVERT: C 1 MET cc_start: 0.7745 (tpp) cc_final: 0.7305 (tpp) REVERT: C 116 MET cc_start: 0.8468 (ppp) cc_final: 0.7326 (ppp) REVERT: C 119 MET cc_start: 0.8614 (tmm) cc_final: 0.7950 (tmm) REVERT: D 40 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7997 (tmm) REVERT: E 848 ASP cc_start: 0.9754 (m-30) cc_final: 0.9418 (p0) outliers start: 43 outliers final: 22 residues processed: 114 average time/residue: 0.2199 time to fit residues: 38.3646 Evaluate side-chains 96 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 79 LEU 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 64 ARG 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 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 116 optimal weight: 0.6980 chunk 124 optimal weight: 0.0170 chunk 112 optimal weight: 0.0670 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 40.0000 chunk 142 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.091337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.064012 restraints weight = 82931.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.064155 restraints weight = 47590.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064221 restraints weight = 37172.058| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13112 Z= 0.123 Angle : 0.632 12.254 18095 Z= 0.325 Chirality : 0.041 0.152 2071 Planarity : 0.004 0.047 2018 Dihedral : 21.696 78.516 2436 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 3.45 % Allowed : 29.94 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1379 helix: 0.89 (0.25), residues: 449 sheet: -0.71 (0.29), residues: 350 loop : -1.19 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 638 HIS 0.003 0.001 HIS C 153 PHE 0.026 0.001 PHE B 215 TYR 0.023 0.001 TYR E 842 ARG 0.003 0.000 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.06406 ( 539) hydrogen bonds : angle 5.43243 ( 1462) SS BOND : bond 0.00490 ( 3) SS BOND : angle 0.87894 ( 6) covalent geometry : bond 0.00253 (13109) covalent geometry : angle 0.63199 (18089) *********************** 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 125 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9480 (tmm) cc_final: 0.9161 (tmm) REVERT: B 199 MET cc_start: 0.6950 (tpt) cc_final: 0.6697 (tpt) REVERT: C 1 MET cc_start: 0.7986 (tpp) cc_final: 0.7747 (tpp) REVERT: C 79 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9440 (tt) REVERT: C 116 MET cc_start: 0.8415 (ppp) cc_final: 0.7365 (ppp) REVERT: C 119 MET cc_start: 0.8626 (tmm) cc_final: 0.8066 (tmm) REVERT: D 1 MET cc_start: 0.8587 (tpt) cc_final: 0.8336 (tpp) REVERT: D 40 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7976 (tmm) REVERT: D 99 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9070 (pp) REVERT: E 457 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: E 742 HIS cc_start: 0.2045 (OUTLIER) cc_final: 0.1739 (t70) REVERT: E 848 ASP cc_start: 0.9716 (m-30) cc_final: 0.9317 (p0) outliers start: 42 outliers final: 18 residues processed: 119 average time/residue: 0.2236 time to fit residues: 40.2921 Evaluate side-chains 99 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 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 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 457 GLN Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 742 HIS 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 130 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 ** 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 = 0.4069 r_free = 0.4069 target = 0.090608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.063682 restraints weight = 82634.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.063591 restraints weight = 43452.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063695 restraints weight = 35241.267| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13112 Z= 0.129 Angle : 0.601 11.012 18095 Z= 0.312 Chirality : 0.040 0.151 2071 Planarity : 0.003 0.043 2018 Dihedral : 21.577 76.208 2436 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.45 % Allowed : 29.94 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1379 helix: 0.87 (0.25), residues: 457 sheet: -0.85 (0.28), residues: 355 loop : -1.15 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 638 HIS 0.003 0.001 HIS E 742 PHE 0.027 0.001 PHE B 215 TYR 0.021 0.001 TYR E 842 ARG 0.003 0.000 ARG E 704 Details of bonding type rmsd hydrogen bonds : bond 0.06056 ( 539) hydrogen bonds : angle 5.19749 ( 1462) SS BOND : bond 0.00407 ( 3) SS BOND : angle 0.85406 ( 6) covalent geometry : bond 0.00274 (13109) covalent geometry : angle 0.60110 (18089) *********************** 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 123 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9531 (OUTLIER) cc_final: 0.9128 (ppp) REVERT: B 154 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9088 (tp) REVERT: B 199 MET cc_start: 0.6630 (tpt) cc_final: 0.6298 (tpt) REVERT: C 54 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.8879 (m) REVERT: C 116 MET cc_start: 0.8465 (ppp) cc_final: 0.7389 (ppp) REVERT: C 119 MET cc_start: 0.8620 (tmm) cc_final: 0.8126 (tmm) REVERT: D 1 MET cc_start: 0.8705 (tpt) cc_final: 0.8396 (tpp) REVERT: D 40 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8086 (tmm) REVERT: D 99 LEU cc_start: 0.9364 (tp) cc_final: 0.9042 (pp) REVERT: E 457 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: E 848 ASP cc_start: 0.9731 (m-30) cc_final: 0.9362 (p0) outliers start: 42 outliers final: 28 residues processed: 118 average time/residue: 0.2067 time to fit residues: 38.2459 Evaluate side-chains 108 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 139 MET 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 215 PHE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 199 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 102 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 457 GLN Chi-restraints excluded: chain E residue 473 SER 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 940 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 8 GLN D 44 HIS E 492 GLN ** E 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.087107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060081 restraints weight = 84163.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.059692 restraints weight = 44327.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.060021 restraints weight = 34834.546| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13112 Z= 0.245 Angle : 0.670 11.191 18095 Z= 0.349 Chirality : 0.041 0.185 2071 Planarity : 0.004 0.049 2018 Dihedral : 21.877 74.853 2436 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 5.17 % Allowed : 28.22 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1379 helix: 0.72 (0.24), residues: 453 sheet: -0.90 (0.28), residues: 351 loop : -1.20 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 707 HIS 0.005 0.001 HIS C 44 PHE 0.035 0.002 PHE B 215 TYR 0.023 0.002 TYR D 249 ARG 0.008 0.001 ARG E 706 Details of bonding type rmsd hydrogen bonds : bond 0.06798 ( 539) hydrogen bonds : angle 5.43418 ( 1462) SS BOND : bond 0.00492 ( 3) SS BOND : angle 1.02572 ( 6) covalent geometry : bond 0.00517 (13109) covalent geometry : angle 0.66952 (18089) *********************** 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 138 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 75 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8939 (mm) REVERT: B 139 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.9105 (ppp) REVERT: B 199 MET cc_start: 0.7084 (tpt) cc_final: 0.6617 (tpt) REVERT: C 54 SER cc_start: 0.9445 (OUTLIER) cc_final: 0.8876 (m) REVERT: C 119 MET cc_start: 0.8634 (tmm) cc_final: 0.8221 (tmm) REVERT: C 229 MET cc_start: 0.8744 (pmt) cc_final: 0.8461 (pmt) REVERT: D 40 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8063 (tmm) REVERT: D 99 LEU cc_start: 0.9473 (tp) cc_final: 0.9217 (pp) REVERT: D 111 VAL cc_start: 0.9584 (OUTLIER) cc_final: 0.9384 (p) REVERT: D 207 PHE cc_start: 0.8711 (m-80) cc_final: 0.8323 (m-80) REVERT: E 457 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: E 848 ASP cc_start: 0.9769 (m-30) cc_final: 0.9430 (p0) outliers start: 63 outliers final: 43 residues processed: 130 average time/residue: 0.2024 time to fit residues: 41.7083 Evaluate side-chains 120 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 71 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 162 CYS 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 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 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 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 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 393 MET Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 457 GLN Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 510 CYS 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 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 984 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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** E 492 GLN ** 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 = 0.4026 r_free = 0.4026 target = 0.087648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.060292 restraints weight = 84342.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.060369 restraints weight = 45298.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060529 restraints weight = 33390.237| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13112 Z= 0.182 Angle : 0.660 15.360 18095 Z= 0.338 Chirality : 0.040 0.125 2071 Planarity : 0.004 0.042 2018 Dihedral : 21.963 74.662 2436 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 4.84 % Allowed : 29.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1379 helix: 0.82 (0.24), residues: 450 sheet: -0.99 (0.27), residues: 357 loop : -1.17 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 28 HIS 0.004 0.001 HIS B 153 PHE 0.034 0.002 PHE B 215 TYR 0.021 0.002 TYR E 842 ARG 0.003 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.05813 ( 539) hydrogen bonds : angle 5.26111 ( 1462) SS BOND : bond 0.00363 ( 3) SS BOND : angle 1.16177 ( 6) covalent geometry : bond 0.00389 (13109) covalent geometry : angle 0.66022 (18089) *********************** 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 133 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 74 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8933 (mm) REVERT: B 139 MET cc_start: 0.9540 (OUTLIER) cc_final: 0.9136 (ppp) REVERT: B 199 MET cc_start: 0.7116 (tpt) cc_final: 0.6649 (tpt) REVERT: C 1 MET cc_start: 0.8087 (tpp) cc_final: 0.7752 (tpp) REVERT: C 54 SER cc_start: 0.9442 (OUTLIER) cc_final: 0.8796 (m) REVERT: C 119 MET cc_start: 0.8615 (tmm) cc_final: 0.8208 (tmm) REVERT: C 229 MET cc_start: 0.8793 (pmt) cc_final: 0.8530 (pmt) REVERT: D 1 MET cc_start: 0.9027 (tpp) cc_final: 0.8415 (tpp) REVERT: D 40 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8014 (tmm) REVERT: D 99 LEU cc_start: 0.9518 (tp) cc_final: 0.9245 (pp) REVERT: D 207 PHE cc_start: 0.8696 (m-80) cc_final: 0.8316 (m-80) REVERT: E 457 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: E 848 ASP cc_start: 0.9769 (m-30) cc_final: 0.9464 (p0) outliers start: 59 outliers final: 39 residues processed: 129 average time/residue: 0.2076 time to fit residues: 41.6502 Evaluate side-chains 116 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 72 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 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 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 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 139 MET Chi-restraints excluded: chain C residue 148 CYS 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 97 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 LYS 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 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 457 GLN Chi-restraints excluded: chain E residue 602 LEU 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 931 LEU Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 984 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 87 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** 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 = 0.4042 r_free = 0.4042 target = 0.088583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061807 restraints weight = 82864.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.061385 restraints weight = 44839.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.061729 restraints weight = 35644.280| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13112 Z= 0.135 Angle : 0.645 12.569 18095 Z= 0.324 Chirality : 0.041 0.174 2071 Planarity : 0.003 0.037 2018 Dihedral : 21.846 74.110 2436 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 4.18 % Allowed : 29.70 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.23), residues: 1379 helix: 1.01 (0.25), residues: 450 sheet: -0.90 (0.27), residues: 369 loop : -1.11 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 638 HIS 0.002 0.001 HIS E 594 PHE 0.032 0.001 PHE B 215 TYR 0.019 0.001 TYR E 842 ARG 0.003 0.000 ARG E 424 Details of bonding type rmsd hydrogen bonds : bond 0.05550 ( 539) hydrogen bonds : angle 5.07186 ( 1462) SS BOND : bond 0.00428 ( 3) SS BOND : angle 1.27793 ( 6) covalent geometry : bond 0.00291 (13109) covalent geometry : angle 0.64506 (18089) *********************** 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 131 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 80 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.9111 (ppp) REVERT: B 199 MET cc_start: 0.6936 (tpt) cc_final: 0.6480 (tpt) REVERT: C 1 MET cc_start: 0.8204 (tpp) cc_final: 0.7882 (tpp) REVERT: C 54 SER cc_start: 0.9447 (OUTLIER) cc_final: 0.8801 (m) REVERT: C 119 MET cc_start: 0.8606 (tmm) cc_final: 0.8252 (tmm) REVERT: C 229 MET cc_start: 0.8903 (pmt) cc_final: 0.8674 (pmt) REVERT: D 1 MET cc_start: 0.9034 (tpp) cc_final: 0.8360 (tpp) REVERT: D 40 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7990 (tmm) REVERT: D 99 LEU cc_start: 0.9461 (tp) cc_final: 0.9200 (pp) REVERT: D 207 PHE cc_start: 0.8721 (m-80) cc_final: 0.8366 (m-80) REVERT: E 457 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: E 848 ASP cc_start: 0.9780 (m-30) cc_final: 0.9470 (p0) outliers start: 51 outliers final: 40 residues processed: 125 average time/residue: 0.2045 time to fit residues: 40.1710 Evaluate side-chains 119 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 75 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 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 162 CYS 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 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 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 89 THR 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 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 457 GLN 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 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 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 105 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.087735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.060893 restraints weight = 83833.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060579 restraints weight = 44785.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.060883 restraints weight = 35263.986| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13112 Z= 0.158 Angle : 0.664 13.773 18095 Z= 0.332 Chirality : 0.040 0.143 2071 Planarity : 0.004 0.038 2018 Dihedral : 21.845 74.032 2436 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 4.59 % Allowed : 29.37 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1379 helix: 1.03 (0.25), residues: 451 sheet: -0.86 (0.27), residues: 369 loop : -1.10 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 847 HIS 0.002 0.001 HIS B 153 PHE 0.032 0.001 PHE B 215 TYR 0.020 0.002 TYR E 842 ARG 0.003 0.000 ARG E 424 Details of bonding type rmsd hydrogen bonds : bond 0.05637 ( 539) hydrogen bonds : angle 5.12349 ( 1462) SS BOND : bond 0.00438 ( 3) SS BOND : angle 1.27774 ( 6) covalent geometry : bond 0.00339 (13109) covalent geometry : angle 0.66405 (18089) *********************** 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 131 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 75 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8933 (mm) REVERT: B 112 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8631 (p) REVERT: B 139 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.9103 (ppp) REVERT: B 199 MET cc_start: 0.7071 (tpt) cc_final: 0.6672 (tpt) REVERT: C 1 MET cc_start: 0.8227 (tpp) cc_final: 0.7965 (tpp) REVERT: C 54 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.8817 (m) REVERT: C 119 MET cc_start: 0.8596 (tmm) cc_final: 0.8260 (tmm) REVERT: C 229 MET cc_start: 0.8897 (pmt) cc_final: 0.8577 (pmt) REVERT: D 40 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7999 (tmm) REVERT: D 99 LEU cc_start: 0.9475 (tp) cc_final: 0.9255 (pp) REVERT: D 207 PHE cc_start: 0.8681 (m-80) cc_final: 0.8317 (m-80) REVERT: E 457 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: E 772 MET cc_start: 0.0436 (mmp) cc_final: -0.2186 (ptt) REVERT: E 848 ASP cc_start: 0.9766 (m-30) cc_final: 0.9467 (p0) outliers start: 56 outliers final: 42 residues processed: 126 average time/residue: 0.2100 time to fit residues: 40.8673 Evaluate side-chains 123 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 75 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 162 CYS 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 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 90 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 148 CYS 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 97 ASP Chi-restraints excluded: chain D residue 102 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 457 GLN 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 814 VAL 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 Chi-restraints excluded: chain E residue 984 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 129 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.087713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.058051 restraints weight = 83516.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.059702 restraints weight = 44586.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.060881 restraints weight = 29883.165| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2968 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= 0.150 Angle : 0.684 14.733 18095 Z= 0.337 Chirality : 0.040 0.147 2071 Planarity : 0.004 0.041 2018 Dihedral : 21.844 73.886 2436 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 4.43 % Allowed : 29.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.23), residues: 1379 helix: 1.04 (0.25), residues: 451 sheet: -0.76 (0.28), residues: 359 loop : -1.14 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 28 HIS 0.005 0.001 HIS E 718 PHE 0.032 0.001 PHE B 215 TYR 0.019 0.002 TYR E 842 ARG 0.003 0.000 ARG E 424 Details of bonding type rmsd hydrogen bonds : bond 0.05501 ( 539) hydrogen bonds : angle 5.08022 ( 1462) SS BOND : bond 0.00692 ( 3) SS BOND : angle 1.41233 ( 6) covalent geometry : bond 0.00324 (13109) covalent geometry : angle 0.68370 (18089) *********************** 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 131 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 77 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8966 (mm) REVERT: B 112 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8796 (p) REVERT: B 139 MET cc_start: 0.9541 (OUTLIER) cc_final: 0.9098 (ppp) REVERT: B 199 MET cc_start: 0.6648 (tpt) cc_final: 0.6175 (tpt) REVERT: B 229 MET cc_start: 0.8187 (ptm) cc_final: 0.7649 (tpp) REVERT: C 1 MET cc_start: 0.8169 (tpp) cc_final: 0.7940 (tpp) REVERT: C 54 SER cc_start: 0.9438 (OUTLIER) cc_final: 0.8779 (m) REVERT: C 119 MET cc_start: 0.8621 (tmm) cc_final: 0.8279 (tmm) REVERT: C 229 MET cc_start: 0.8869 (pmt) cc_final: 0.8570 (pmt) REVERT: D 1 MET cc_start: 0.9056 (tpp) cc_final: 0.8395 (tpp) REVERT: D 40 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7973 (tmm) REVERT: D 207 PHE cc_start: 0.8674 (m-80) cc_final: 0.8339 (m-80) REVERT: E 457 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: E 472 LEU cc_start: 0.9709 (pt) cc_final: 0.9318 (pp) REVERT: E 772 MET cc_start: 0.0238 (mmp) cc_final: -0.1945 (ptt) REVERT: E 848 ASP cc_start: 0.9786 (m-30) cc_final: 0.9527 (p0) outliers start: 54 outliers final: 44 residues processed: 126 average time/residue: 0.2068 time to fit residues: 41.2041 Evaluate side-chains 126 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 76 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 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 162 CYS 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 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 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 148 CYS 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 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 457 GLN 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 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 964 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 0.0020 chunk 129 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 145 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 overall best weight: 3.2794 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.085941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.058714 restraints weight = 84173.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.058750 restraints weight = 47318.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.058915 restraints weight = 33058.477| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13112 Z= 0.207 Angle : 0.718 15.676 18095 Z= 0.355 Chirality : 0.042 0.312 2071 Planarity : 0.004 0.038 2018 Dihedral : 21.961 74.873 2436 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 4.43 % Allowed : 29.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1379 helix: 0.88 (0.24), residues: 453 sheet: -0.91 (0.27), residues: 363 loop : -1.16 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 638 HIS 0.008 0.001 HIS C 44 PHE 0.036 0.002 PHE B 215 TYR 0.024 0.002 TYR D 249 ARG 0.007 0.001 ARG E 668 Details of bonding type rmsd hydrogen bonds : bond 0.06080 ( 539) hydrogen bonds : angle 5.22580 ( 1462) SS BOND : bond 0.00451 ( 3) SS BOND : angle 1.18887 ( 6) covalent geometry : bond 0.00445 (13109) covalent geometry : angle 0.71767 (18089) ********************** 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 127 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 73 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8961 (mm) REVERT: B 112 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 139 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9084 (ppp) REVERT: B 199 MET cc_start: 0.6798 (tpt) cc_final: 0.6207 (tpt) REVERT: B 229 MET cc_start: 0.8252 (ptm) cc_final: 0.7754 (tpp) REVERT: C 54 SER cc_start: 0.9430 (OUTLIER) cc_final: 0.8799 (m) REVERT: C 119 MET cc_start: 0.8590 (tmm) cc_final: 0.8262 (tmm) REVERT: C 229 MET cc_start: 0.8859 (pmt) cc_final: 0.8546 (pmt) REVERT: D 1 MET cc_start: 0.9225 (tpp) cc_final: 0.8550 (tpp) REVERT: D 40 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7993 (tmm) REVERT: D 207 PHE cc_start: 0.8733 (m-80) cc_final: 0.8415 (m-80) REVERT: E 457 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: E 472 LEU cc_start: 0.9755 (pt) cc_final: 0.9540 (pt) REVERT: E 772 MET cc_start: 0.0554 (mmp) cc_final: -0.1966 (ptt) REVERT: E 848 ASP cc_start: 0.9793 (m-30) cc_final: 0.9509 (p0) outliers start: 54 outliers final: 44 residues processed: 123 average time/residue: 0.2134 time to fit residues: 40.2210 Evaluate side-chains 122 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 72 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 162 CYS 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 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 90 LEU Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 148 CYS 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 97 ASP Chi-restraints excluded: chain D residue 102 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 407 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 457 GLN 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 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 964 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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** B 246 HIS ** D 131 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 = 0.3975 r_free = 0.3975 target = 0.084059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057023 restraints weight = 84906.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056832 restraints weight = 48640.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.057011 restraints weight = 36104.998| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13112 Z= 0.257 Angle : 0.767 14.749 18095 Z= 0.384 Chirality : 0.042 0.177 2071 Planarity : 0.004 0.041 2018 Dihedral : 22.277 81.958 2436 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 4.59 % Allowed : 29.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1379 helix: 0.80 (0.25), residues: 444 sheet: -1.07 (0.28), residues: 349 loop : -1.18 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 847 HIS 0.005 0.001 HIS C 44 PHE 0.040 0.002 PHE B 215 TYR 0.027 0.002 TYR D 249 ARG 0.014 0.001 ARG E 648 Details of bonding type rmsd hydrogen bonds : bond 0.06718 ( 539) hydrogen bonds : angle 5.46782 ( 1462) SS BOND : bond 0.00534 ( 3) SS BOND : angle 1.10249 ( 6) covalent geometry : bond 0.00547 (13109) covalent geometry : angle 0.76692 (18089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4449.25 seconds wall clock time: 78 minutes 47.51 seconds (4727.51 seconds total)