Starting phenix.real_space_refine on Thu Aug 6 01:20:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl7_45664/08_2026/9cl7_45664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl7_45664/08_2026/9cl7_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_45664/08_2026/9cl7_45664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl7_45664/08_2026/9cl7_45664.map" model { file = "/net/cci-nas-00/data/ceres_data/9cl7_45664/08_2026/9cl7_45664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl7_45664/08_2026/9cl7_45664.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 75 5.16 5 C 7742 2.51 5 N 2187 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12714 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 949 Classifications: {'DNA': 46} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 817 Classifications: {'DNA': 40} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 39} Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "E" Number of atoms: 4924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4924 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 4 Time building chain proxies: 2.13, per 1000 atoms: 0.17 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: 0.94 Conformation dependent library (CDL) restraints added in 489.7 milliseconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 41.4% alpha, 18.2% beta 29 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.10 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: 1.96 Time building geometry restraints manager: 1.22 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=" C3' DG F 11 " pdb=" C2' DG F 11 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG A 34 " pdb=" C2' DG A 34 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.43e+00 bond pdb=" C3' DT F 24 " pdb=" C2' DT F 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.40e+00 bond pdb=" C3' DA A 19 " pdb=" C2' DA A 19 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.35e+00 bond pdb=" C3' DG A 23 " pdb=" C2' DG A 23 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.35e+00 ... (remaining 13104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 17957 3.13 - 6.25: 105 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=" N3 DT F 15 " pdb=" C4 DT F 15 " pdb=" O4 DT F 15 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+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=" N3 DT A 35 " pdb=" C4 DT A 35 " pdb=" O4 DT A 35 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT F 4 " pdb=" C4 DT F 4 " pdb=" O4 DT F 4 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+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: 1366 0.038 - 0.075: 495 0.075 - 0.113: 185 0.113 - 0.150: 22 0.150 - 0.188: 3 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=" C3' DC F 14 " pdb=" C4' DC F 14 " pdb=" O3' DC F 14 " pdb=" C2' DC F 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 2068 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 215 " 0.020 2.00e-02 2.50e+03 1.66e-02 4.81e+00 pdb=" CG PHE B 215 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 215 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 215 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 215 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 215 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 215 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 233 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 234 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C THR C 89 " 0.028 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 90 " -0.009 2.00e-02 2.50e+03 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 795 2.72 - 3.26: 13465 3.26 - 3.81: 22828 3.81 - 4.35: 26329 4.35 - 4.90: 40479 Nonbonded interactions: 103896 Sorted by model distance: nonbonded pdb=" O ARG E 721 " pdb=" OG1 THR E 725 " model vdw 2.174 3.040 nonbonded pdb=" O SER C 31 " pdb=" OH TYR C 60 " model vdw 2.186 3.040 nonbonded pdb=" O LEU E 550 " pdb=" OG SER E 553 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP D 41 " pdb=" OG SER D 43 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP B 41 " pdb=" OH TYR B 211 " model vdw 2.216 3.040 ... (remaining 103891 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.004 0.053 13112 Z= 0.292 Angle : 0.746 15.635 18095 Z= 0.458 Chirality : 0.044 0.188 2071 Planarity : 0.003 0.051 2018 Dihedral : 21.866 89.983 5107 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 0.25 % Allowed : 35.19 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.23), residues: 1379 helix: 0.56 (0.25), residues: 440 sheet: -0.80 (0.28), residues: 363 loop : -1.20 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 542 TYR 0.011 0.001 TYR D 249 PHE 0.037 0.002 PHE B 215 TRP 0.011 0.001 TRP E 708 HIS 0.003 0.001 HIS E 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.29 (13109) covalent geometry : angle 0.74644 / 0.46 (18089) SS BOND : bond 0.00203 / 0.11 ( 3) SS BOND : angle 0.82350 / 1.69 ( 6) hydrogen bonds : bond 0.24494 / 26.70 ( 539) hydrogen bonds : angle 8.85765 / 11.26 ( 1462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.429 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: 0.0844 time to fit residues: 11.3983 Evaluate side-chains 79 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN D 44 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 = 0.4064 r_free = 0.4064 target = 0.090241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.063843 restraints weight = 82419.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.062954 restraints weight = 45663.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.063658 restraints weight = 35835.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.063552 restraints weight = 30661.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.063655 restraints weight = 29618.980| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13112 Z= 0.168 Angle : 0.676 10.894 18095 Z= 0.361 Chirality : 0.043 0.173 2071 Planarity : 0.004 0.048 2018 Dihedral : 22.055 81.032 2438 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 3.36 % Allowed : 31.01 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1379 helix: 0.51 (0.24), residues: 462 sheet: -0.67 (0.29), residues: 352 loop : -1.22 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 658 TYR 0.026 0.002 TYR E 842 PHE 0.029 0.001 PHE B 215 TRP 0.008 0.001 TRP E 919 HIS 0.004 0.001 HIS E 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (13109) covalent geometry : angle 0.67621 / 0.36 (18089) SS BOND : bond 0.00259 / 0.13 ( 3) SS BOND : angle 0.82715 / 1.53 ( 6) hydrogen bonds : bond 0.07882 / 7.99 ( 539) hydrogen bonds : angle 6.39225 / 8.08 ( 1462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 199 MET cc_start: 0.7054 (tpt) cc_final: 0.6728 (tpt) REVERT: C 1 MET cc_start: 0.7532 (tpp) cc_final: 0.7130 (tpp) REVERT: C 54 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.8925 (m) REVERT: C 116 MET cc_start: 0.8490 (ppp) cc_final: 0.7360 (ppp) REVERT: C 119 MET cc_start: 0.8597 (tmm) cc_final: 0.7965 (tmm) REVERT: D 40 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7926 (tmm) REVERT: E 848 ASP cc_start: 0.9706 (m-30) cc_final: 0.9299 (p0) outliers start: 41 outliers final: 21 residues processed: 116 average time/residue: 0.0816 time to fit residues: 14.8392 Evaluate side-chains 97 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 54 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 612 LEU Chi-restraints excluded: chain E residue 814 VAL Chi-restraints excluded: chain E residue 872 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 20 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 0.0170 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.091088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.064092 restraints weight = 83035.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.063977 restraints weight = 46841.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.064357 restraints weight = 33292.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.064366 restraints weight = 29161.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.064434 restraints weight = 27508.800| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 13112 Z= 0.128 Angle : 0.648 11.471 18095 Z= 0.338 Chirality : 0.043 0.256 2071 Planarity : 0.004 0.047 2018 Dihedral : 21.961 79.252 2436 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 3.36 % Allowed : 30.35 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.23), residues: 1379 helix: 0.72 (0.24), residues: 449 sheet: -0.67 (0.29), residues: 351 loop : -1.22 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 64 TYR 0.025 0.002 TYR E 842 PHE 0.029 0.001 PHE B 215 TRP 0.012 0.001 TRP C 28 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (13109) covalent geometry : angle 0.64757 / 0.34 (18089) SS BOND : bond 0.00677 / 0.34 ( 3) SS BOND : angle 0.81064 / 1.31 ( 6) hydrogen bonds : bond 0.07244 / 7.27 ( 539) hydrogen bonds : angle 5.87812 / 7.45 ( 1462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9491 (tmm) cc_final: 0.9148 (tmm) REVERT: B 199 MET cc_start: 0.7142 (tpt) cc_final: 0.6853 (tpt) REVERT: C 1 MET cc_start: 0.7860 (tpp) cc_final: 0.7518 (tpp) REVERT: C 54 SER cc_start: 0.9496 (OUTLIER) cc_final: 0.8884 (m) REVERT: C 116 MET cc_start: 0.8435 (ppp) cc_final: 0.7423 (ppp) REVERT: C 119 MET cc_start: 0.8628 (tmm) cc_final: 0.8086 (tmm) REVERT: D 40 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7843 (tmm) REVERT: E 457 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: E 848 ASP cc_start: 0.9698 (m-30) cc_final: 0.9282 (p0) outliers start: 41 outliers final: 22 residues processed: 117 average time/residue: 0.0759 time to fit residues: 14.3704 Evaluate side-chains 100 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 54 SER Chi-restraints excluded: chain C residue 112 SER 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 78 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 457 GLN Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 814 VAL Chi-restraints excluded: chain E residue 872 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 87 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 103 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN D 8 GLN ** 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 = 0.4072 r_free = 0.4072 target = 0.090749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.063699 restraints weight = 82711.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063326 restraints weight = 47823.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063654 restraints weight = 33726.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063726 restraints weight = 29880.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.063796 restraints weight = 27817.436| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13112 Z= 0.126 Angle : 0.626 11.148 18095 Z= 0.326 Chirality : 0.042 0.307 2071 Planarity : 0.003 0.045 2018 Dihedral : 21.928 78.360 2436 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.53 % Allowed : 29.70 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.23), residues: 1379 helix: 0.80 (0.24), residues: 449 sheet: -0.88 (0.28), residues: 365 loop : -1.14 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 424 TYR 0.023 0.001 TYR E 842 PHE 0.028 0.001 PHE B 215 TRP 0.010 0.001 TRP E 638 HIS 0.005 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (13109) covalent geometry : angle 0.62593 / 0.33 (18089) SS BOND : bond 0.00567 / 0.28 ( 3) SS BOND : angle 0.77934 / 1.38 ( 6) hydrogen bonds : bond 0.06718 / 6.70 ( 539) hydrogen bonds : angle 5.52929 / 7.04 ( 1462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9505 (tmm) cc_final: 0.9142 (tmm) REVERT: B 199 MET cc_start: 0.6947 (tpt) cc_final: 0.6634 (tpt) REVERT: B 229 MET cc_start: 0.8373 (ppp) cc_final: 0.8124 (ppp) REVERT: B 244 MET cc_start: 0.8483 (tmm) cc_final: 0.8170 (tmm) REVERT: C 1 MET cc_start: 0.7988 (tpp) cc_final: 0.7748 (tpp) REVERT: C 54 SER cc_start: 0.9500 (OUTLIER) cc_final: 0.8895 (m) REVERT: C 119 MET cc_start: 0.8633 (tmm) cc_final: 0.8080 (tmm) REVERT: D 40 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7985 (tmm) REVERT: D 99 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9091 (pp) REVERT: E 457 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: E 848 ASP cc_start: 0.9725 (m-30) cc_final: 0.9345 (p0) outliers start: 43 outliers final: 30 residues processed: 118 average time/residue: 0.0804 time to fit residues: 15.0179 Evaluate side-chains 110 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain B residue 79 LEU 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 207 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 99 LEU 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 441 LEU Chi-restraints excluded: chain E residue 457 GLN Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 710 ARG Chi-restraints excluded: chain E residue 814 VAL Chi-restraints excluded: chain E residue 872 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 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 = 0.4043 r_free = 0.4043 target = 0.088974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.061371 restraints weight = 83953.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.061441 restraints weight = 47059.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.061500 restraints weight = 34419.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061532 restraints weight = 29962.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061808 restraints weight = 28807.007| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13112 Z= 0.198 Angle : 0.659 10.708 18095 Z= 0.340 Chirality : 0.041 0.217 2071 Planarity : 0.004 0.044 2018 Dihedral : 22.012 77.301 2436 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 4.68 % Allowed : 29.12 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.23), residues: 1379 helix: 0.82 (0.25), residues: 451 sheet: -0.97 (0.27), residues: 367 loop : -1.07 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.022 0.002 TYR E 842 PHE 0.030 0.001 PHE B 215 TRP 0.010 0.001 TRP C 28 HIS 0.005 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (13109) covalent geometry : angle 0.65928 / 0.34 (18089) SS BOND : bond 0.00496 / 0.26 ( 3) SS BOND : angle 0.89274 / 1.41 ( 6) hydrogen bonds : bond 0.06862 / 7.04 ( 539) hydrogen bonds : angle 5.53989 / 7.05 ( 1462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 76 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.9275 (tmm) REVERT: B 199 MET cc_start: 0.6871 (tpt) cc_final: 0.6407 (tpt) REVERT: B 244 MET cc_start: 0.8523 (tmm) cc_final: 0.8201 (tmm) REVERT: C 1 MET cc_start: 0.7890 (tpp) cc_final: 0.7683 (tpp) REVERT: C 54 SER cc_start: 0.9479 (OUTLIER) cc_final: 0.8903 (m) REVERT: C 119 MET cc_start: 0.8648 (tmm) cc_final: 0.8136 (tmm) REVERT: C 229 MET cc_start: 0.8794 (pmt) cc_final: 0.8511 (pmt) REVERT: D 1 MET cc_start: 0.8829 (tpp) cc_final: 0.8237 (tpp) REVERT: D 40 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7972 (tmm) REVERT: E 457 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: E 848 ASP cc_start: 0.9755 (m-30) cc_final: 0.9433 (p0) outliers start: 57 outliers final: 40 residues processed: 125 average time/residue: 0.0880 time to fit residues: 16.7036 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 : 0.431 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain B residue 79 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 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 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 195 VAL 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 89 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 LYS 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 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 555 THR Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 612 LEU Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 710 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 103 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.090578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060725 restraints weight = 82338.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.062436 restraints weight = 43298.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.063796 restraints weight = 29441.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.064593 restraints weight = 23166.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.064746 restraints weight = 19985.581| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13112 Z= 0.118 Angle : 0.666 14.180 18095 Z= 0.333 Chirality : 0.043 0.282 2071 Planarity : 0.003 0.043 2018 Dihedral : 22.009 76.151 2436 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.53 % Allowed : 29.37 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1379 helix: 0.85 (0.24), residues: 451 sheet: -0.82 (0.27), residues: 359 loop : -1.11 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 668 TYR 0.024 0.002 TYR E 842 PHE 0.030 0.001 PHE B 215 TRP 0.011 0.001 TRP E 638 HIS 0.004 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (13109) covalent geometry : angle 0.66574 / 0.33 (18089) SS BOND : bond 0.00503 / 0.26 ( 3) SS BOND : angle 1.24743 / 2.15 ( 6) hydrogen bonds : bond 0.06253 / 6.23 ( 539) hydrogen bonds : angle 5.32748 / 6.84 ( 1462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 82 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.9167 (tmm) REVERT: B 199 MET cc_start: 0.6852 (tpt) cc_final: 0.6131 (tpt) REVERT: B 244 MET cc_start: 0.8474 (tmm) cc_final: 0.8211 (tmm) REVERT: C 40 MET cc_start: 0.8659 (ttm) cc_final: 0.8423 (ttm) REVERT: C 54 SER cc_start: 0.9476 (OUTLIER) cc_final: 0.8861 (m) REVERT: C 119 MET cc_start: 0.8594 (tmm) cc_final: 0.8100 (tmm) REVERT: D 1 MET cc_start: 0.8731 (tpp) cc_final: 0.8059 (tpp) REVERT: D 40 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7904 (tmm) REVERT: D 99 LEU cc_start: 0.9391 (tp) cc_final: 0.9024 (pp) REVERT: E 457 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: E 848 ASP cc_start: 0.9774 (m-30) cc_final: 0.9496 (p0) outliers start: 43 outliers final: 29 residues processed: 117 average time/residue: 0.0822 time to fit residues: 15.3569 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 : 0.446 ------------------------------------------------------------------------------- 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 125 GLN Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 195 VAL 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 78 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 457 GLN Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 8 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 30 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4038 r_free = 0.4038 target = 0.088616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.061243 restraints weight = 83919.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.061224 restraints weight = 46431.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.061447 restraints weight = 34705.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061360 restraints weight = 33000.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061403 restraints weight = 29378.983| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13112 Z= 0.203 Angle : 0.708 14.192 18095 Z= 0.357 Chirality : 0.042 0.187 2071 Planarity : 0.004 0.042 2018 Dihedral : 22.027 75.524 2436 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 4.35 % Allowed : 29.70 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1379 helix: 0.92 (0.25), residues: 453 sheet: -0.87 (0.27), residues: 363 loop : -1.15 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 704 TYR 0.021 0.002 TYR E 842 PHE 0.029 0.002 PHE B 215 TRP 0.010 0.001 TRP E 847 HIS 0.006 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (13109) covalent geometry : angle 0.70708 / 0.36 (18089) SS BOND : bond 0.00688 / 0.35 ( 3) SS BOND : angle 2.06080 / 4.11 ( 6) hydrogen bonds : bond 0.06564 / 6.77 ( 539) hydrogen bonds : angle 5.40607 / 6.92 ( 1462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 75 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9215 (tmm) REVERT: B 199 MET cc_start: 0.7205 (tpt) cc_final: 0.6745 (tpt) REVERT: B 244 MET cc_start: 0.8487 (tmm) cc_final: 0.8257 (tmm) REVERT: C 54 SER cc_start: 0.9459 (OUTLIER) cc_final: 0.8881 (m) REVERT: C 119 MET cc_start: 0.8613 (tmm) cc_final: 0.8255 (tmm) REVERT: C 229 MET cc_start: 0.8815 (pmt) cc_final: 0.8544 (pmt) REVERT: D 1 MET cc_start: 0.8899 (tpp) cc_final: 0.8306 (tpp) REVERT: D 40 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8008 (tmm) REVERT: E 457 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: E 848 ASP cc_start: 0.9763 (m-30) cc_final: 0.9405 (p0) outliers start: 53 outliers final: 39 residues processed: 123 average time/residue: 0.0905 time to fit residues: 17.4228 Evaluate side-chains 117 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 74 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 73 THR 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 215 PHE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 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 555 THR Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 59 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 0.0980 overall best weight: 0.4480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.090417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060471 restraints weight = 82024.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.062290 restraints weight = 43390.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063574 restraints weight = 29632.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.064444 restraints weight = 23308.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.064597 restraints weight = 19995.623| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13112 Z= 0.119 Angle : 0.699 13.120 18095 Z= 0.345 Chirality : 0.043 0.188 2071 Planarity : 0.004 0.046 2018 Dihedral : 21.992 74.443 2436 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 3.69 % Allowed : 30.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.23), residues: 1379 helix: 0.89 (0.25), residues: 457 sheet: -0.87 (0.28), residues: 345 loop : -1.19 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 704 TYR 0.022 0.002 TYR E 842 PHE 0.031 0.001 PHE B 215 TRP 0.011 0.001 TRP C 28 HIS 0.005 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (13109) covalent geometry : angle 0.69790 / 0.34 (18089) SS BOND : bond 0.00578 / 0.30 ( 3) SS BOND : angle 1.98422 / 3.98 ( 6) hydrogen bonds : bond 0.06026 / 6.00 ( 539) hydrogen bonds : angle 5.19455 / 6.68 ( 1462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8707 (tm-30) REVERT: B 125 GLN cc_start: 0.8157 (mm110) cc_final: 0.7943 (mm110) REVERT: B 139 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9169 (tmm) REVERT: B 244 MET cc_start: 0.8484 (tmm) cc_final: 0.8275 (tmm) REVERT: C 54 SER cc_start: 0.9401 (OUTLIER) cc_final: 0.8798 (m) REVERT: C 119 MET cc_start: 0.8598 (tmm) cc_final: 0.8185 (tmm) REVERT: D 40 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7953 (tmm) REVERT: D 99 LEU cc_start: 0.9362 (tp) cc_final: 0.9033 (pp) REVERT: D 207 PHE cc_start: 0.8643 (m-80) cc_final: 0.8239 (m-80) REVERT: E 457 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: E 848 ASP cc_start: 0.9790 (m-30) cc_final: 0.9452 (p0) outliers start: 45 outliers final: 32 residues processed: 118 average time/residue: 0.0808 time to fit residues: 15.0329 Evaluate side-chains 114 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 49 GLN 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 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER 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 78 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain 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 661 THR Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 0.0470 chunk 73 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 7 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 overall best weight: 1.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4058 r_free = 0.4058 target = 0.089614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.059552 restraints weight = 82895.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.061208 restraints weight = 43886.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 97)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.062710 restraints weight = 29920.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.063388 restraints weight = 23571.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063530 restraints weight = 20428.775| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13112 Z= 0.136 Angle : 0.712 14.736 18095 Z= 0.351 Chirality : 0.042 0.156 2071 Planarity : 0.004 0.042 2018 Dihedral : 21.947 73.992 2436 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.36 % Allowed : 30.84 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1379 helix: 0.91 (0.25), residues: 459 sheet: -0.84 (0.28), residues: 347 loop : -1.23 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 547 TYR 0.021 0.002 TYR E 842 PHE 0.028 0.001 PHE B 215 TRP 0.012 0.001 TRP E 847 HIS 0.005 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (13109) covalent geometry : angle 0.71167 / 0.35 (18089) SS BOND : bond 0.00429 / 0.22 ( 3) SS BOND : angle 1.61024 / 3.09 ( 6) hydrogen bonds : bond 0.06064 / 6.16 ( 539) hydrogen bonds : angle 5.22608 / 6.68 ( 1462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8724 (tm-30) REVERT: B 125 GLN cc_start: 0.8152 (mm110) cc_final: 0.7878 (mm-40) REVERT: B 139 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9176 (tmm) REVERT: C 54 SER cc_start: 0.9455 (OUTLIER) cc_final: 0.8859 (m) REVERT: C 119 MET cc_start: 0.8565 (tmm) cc_final: 0.8177 (tmm) REVERT: C 126 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8847 (mp) REVERT: C 199 MET cc_start: 0.8123 (tpp) cc_final: 0.7820 (tpp) REVERT: D 1 MET cc_start: 0.8820 (tpp) cc_final: 0.8213 (tpp) REVERT: D 40 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7965 (tmm) REVERT: D 99 LEU cc_start: 0.9333 (tp) cc_final: 0.9027 (pp) REVERT: E 457 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6948 (pm20) REVERT: E 472 LEU cc_start: 0.9621 (pp) cc_final: 0.9371 (pp) REVERT: E 848 ASP cc_start: 0.9774 (m-30) cc_final: 0.9485 (p0) outliers start: 41 outliers final: 32 residues processed: 114 average time/residue: 0.0822 time to fit residues: 14.8716 Evaluate side-chains 115 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 GLN 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 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 215 PHE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 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 78 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 457 GLN Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 1 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 chunk 75 optimal weight: 0.0980 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 144 optimal weight: 5.9990 chunk 30 optimal weight: 0.0040 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4083 r_free = 0.4083 target = 0.091040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.063144 restraints weight = 82365.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.064603 restraints weight = 44244.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.065198 restraints weight = 29396.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.065089 restraints weight = 30859.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.065055 restraints weight = 23051.656| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13112 Z= 0.116 Angle : 0.724 15.086 18095 Z= 0.354 Chirality : 0.042 0.182 2071 Planarity : 0.004 0.042 2018 Dihedral : 21.880 73.577 2436 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 2.87 % Allowed : 31.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.23), residues: 1379 helix: 0.88 (0.25), residues: 458 sheet: -0.72 (0.28), residues: 345 loop : -1.23 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 879 TYR 0.020 0.001 TYR E 842 PHE 0.029 0.001 PHE B 215 TRP 0.013 0.001 TRP E 708 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (13109) covalent geometry : angle 0.72384 / 0.35 (18089) SS BOND : bond 0.00429 / 0.24 ( 3) SS BOND : angle 1.37331 / 2.54 ( 6) hydrogen bonds : bond 0.05981 / 5.91 ( 539) hydrogen bonds : angle 5.05535 / 6.46 ( 1462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8727 (tm-30) REVERT: B 125 GLN cc_start: 0.8087 (mm110) cc_final: 0.7832 (mm-40) REVERT: B 139 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.9200 (tmm) REVERT: B 199 MET cc_start: 0.7116 (tpt) cc_final: 0.5975 (mmm) REVERT: C 1 MET cc_start: 0.8093 (tpp) cc_final: 0.7751 (tpp) REVERT: C 54 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.8807 (m) REVERT: C 119 MET cc_start: 0.8599 (tmm) cc_final: 0.8251 (tmm) REVERT: C 126 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8890 (mp) REVERT: C 199 MET cc_start: 0.8046 (tpp) cc_final: 0.7799 (tpp) REVERT: D 1 MET cc_start: 0.8697 (tpp) cc_final: 0.8180 (tpp) REVERT: D 40 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8023 (tmm) REVERT: D 99 LEU cc_start: 0.9303 (tp) cc_final: 0.9026 (pp) REVERT: E 472 LEU cc_start: 0.9620 (pp) cc_final: 0.9362 (pp) REVERT: E 848 ASP cc_start: 0.9733 (m-30) cc_final: 0.9410 (p0) outliers start: 35 outliers final: 26 residues processed: 113 average time/residue: 0.0784 time to fit residues: 14.3837 Evaluate side-chains 108 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 GLN 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 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 215 PHE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 940 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 111 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 3 optimal weight: 40.0000 chunk 70 optimal weight: 0.2980 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4065 r_free = 0.4065 target = 0.089929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.062146 restraints weight = 82883.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.063492 restraints weight = 44044.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062879 restraints weight = 29393.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.063058 restraints weight = 31102.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063092 restraints weight = 25990.196| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13112 Z= 0.133 Angle : 0.715 15.153 18095 Z= 0.353 Chirality : 0.042 0.207 2071 Planarity : 0.004 0.036 2018 Dihedral : 21.850 73.312 2436 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 2.63 % Allowed : 31.42 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.23), residues: 1379 helix: 0.99 (0.25), residues: 454 sheet: -0.73 (0.28), residues: 347 loop : -1.27 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 542 TYR 0.020 0.001 TYR E 842 PHE 0.027 0.001 PHE B 215 TRP 0.016 0.001 TRP E 847 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (13109) covalent geometry : angle 0.71485 / 0.35 (18089) SS BOND : bond 0.00281 / 0.14 ( 3) SS BOND : angle 1.24916 / 2.21 ( 6) hydrogen bonds : bond 0.05924 / 5.95 ( 539) hydrogen bonds : angle 5.07423 / 6.48 ( 1462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.70 seconds wall clock time: 43 minutes 13.12 seconds (2593.12 seconds total)