Starting phenix.real_space_refine on Fri Jul 3 07:03:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl7_45664/07_2026/9cl7_45664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl7_45664/07_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_45664/07_2026/9cl7_45664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl7_45664/07_2026/9cl7_45664.map" model { file = "/net/cci-nas-00/data/ceres_data/9cl7_45664/07_2026/9cl7_45664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl7_45664/07_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-dev-6108/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: 2.78, per 1000 atoms: 0.22 Number of scatterers: 12714 At special positions: 0 Unit cell: (102.03, 111.696, 147.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 86 15.00 O 2624 8.00 N 2187 7.00 C 7742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 519.6 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: 1.63 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: 2.61 Time building geometry restraints manager: 1.33 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: 1.240 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- 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 : 0.745 15.635 18095 Z= 0.456 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 0.74505 / 0.46 (18089) SS BOND : bond 0.00203 / 0.11 ( 3) SS BOND : angle 0.82350 / 1.69 ( 6) hydrogen bonds : bond 0.24494 / 26.59 ( 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 : 0.438 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: 0.0865 time to fit residues: 11.5790 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 : 0.334 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.090220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.063860 restraints weight = 82411.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.062932 restraints weight = 45714.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.063730 restraints weight = 35897.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.063533 restraints weight = 30534.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.063649 restraints weight = 29441.914| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0843 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= 0.165 Angle : 0.670 11.070 18095 Z= 0.358 Chirality : 0.043 0.174 2071 Planarity : 0.004 0.049 2018 Dihedral : 22.060 81.237 2438 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 3.20 % Allowed : 31.34 % Favored : 65.46 % 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: -0.77 (0.23), residues: 1379 helix: 0.54 (0.24), residues: 461 sheet: -0.66 (0.29), residues: 352 loop : -1.19 (0.26), residues: 566 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 0.028 0.001 PHE B 215 TRP 0.008 0.001 TRP E 906 HIS 0.003 0.001 HIS E 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (13109) covalent geometry : angle 0.66967 / 0.36 (18089) SS BOND : bond 0.00248 / 0.13 ( 3) SS BOND : angle 0.82923 / 1.51 ( 6) hydrogen bonds : bond 0.08154 / 8.24 ( 539) hydrogen bonds : angle 6.47361 / 8.19 ( 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 118 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 MET cc_start: 0.7082 (tpt) cc_final: 0.6866 (tpt) REVERT: C 1 MET cc_start: 0.7513 (tpp) cc_final: 0.7121 (tpp) REVERT: C 54 SER cc_start: 0.9541 (OUTLIER) cc_final: 0.8911 (m) REVERT: C 116 MET cc_start: 0.8485 (ppp) cc_final: 0.7335 (ppp) REVERT: E 848 ASP cc_start: 0.9703 (m-30) cc_final: 0.9295 (p0) outliers start: 39 outliers final: 20 residues processed: 115 average time/residue: 0.0892 time to fit residues: 16.0862 Evaluate side-chains 96 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 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 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 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: 0.0980 chunk 20 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.0570 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 93 optimal weight: 0.5980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.091686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.064721 restraints weight = 82760.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.064845 restraints weight = 48310.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.065091 restraints weight = 36079.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.065135 restraints weight = 31411.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.065207 restraints weight = 29424.294| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 13112 Z= 0.126 Angle : 0.650 11.703 18095 Z= 0.339 Chirality : 0.043 0.241 2071 Planarity : 0.004 0.047 2018 Dihedral : 21.983 79.656 2436 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 3.04 % Allowed : 30.68 % 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: -0.64 (0.29), residues: 351 loop : -1.24 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 64 TYR 0.025 0.001 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 0.00238 / 0.13 (13109) covalent geometry : angle 0.64988 / 0.34 (18089) SS BOND : bond 0.00598 / 0.31 ( 3) SS BOND : angle 0.76353 / 1.36 ( 6) hydrogen bonds : bond 0.07258 / 7.17 ( 539) hydrogen bonds : angle 5.83816 / 7.41 ( 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 118 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7831 (tpp) cc_final: 0.7473 (tpp) REVERT: C 54 SER cc_start: 0.9513 (OUTLIER) cc_final: 0.8885 (m) REVERT: C 116 MET cc_start: 0.8439 (ppp) cc_final: 0.7513 (ppp) REVERT: C 119 MET cc_start: 0.8552 (tmm) cc_final: 0.8176 (tmm) REVERT: D 1 MET cc_start: 0.8481 (tpt) cc_final: 0.8133 (mmm) REVERT: D 40 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8004 (tmm) REVERT: E 457 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: E 848 ASP cc_start: 0.9681 (m-30) cc_final: 0.9262 (p0) outliers start: 37 outliers final: 18 residues processed: 114 average time/residue: 0.0823 time to fit residues: 14.9146 Evaluate side-chains 98 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 112 SER 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 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: 2.9990 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.089855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.063241 restraints weight = 83196.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062258 restraints weight = 47103.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.063162 restraints weight = 35794.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.062832 restraints weight = 30224.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.063019 restraints weight = 27912.907| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13112 Z= 0.166 Angle : 0.639 11.632 18095 Z= 0.333 Chirality : 0.042 0.267 2071 Planarity : 0.004 0.046 2018 Dihedral : 21.991 78.849 2436 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 3.69 % Allowed : 29.53 % 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: 0.84 (0.25), residues: 449 sheet: -0.99 (0.27), residues: 371 loop : -1.09 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 149 TYR 0.023 0.002 TYR E 842 PHE 0.027 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 0.00337 / 0.17 (13109) covalent geometry : angle 0.63935 / 0.33 (18089) SS BOND : bond 0.00575 / 0.30 ( 3) SS BOND : angle 0.76171 / 1.35 ( 6) hydrogen bonds : bond 0.06985 / 7.03 ( 539) hydrogen bonds : angle 5.60105 / 7.13 ( 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: 45 poor density : 78 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: 0.8496 (tmm) cc_final: 0.8153 (tmm) REVERT: C 1 MET cc_start: 0.7978 (tpp) cc_final: 0.7740 (tpp) REVERT: C 54 SER cc_start: 0.9460 (OUTLIER) cc_final: 0.8862 (m) REVERT: C 119 MET cc_start: 0.8577 (tmm) cc_final: 0.8135 (tmm) REVERT: E 457 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: E 848 ASP cc_start: 0.9725 (m-30) cc_final: 0.9331 (p0) outliers start: 45 outliers final: 32 residues processed: 116 average time/residue: 0.0796 time to fit residues: 14.5958 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 : 0.321 ------------------------------------------------------------------------------- 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 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 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 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 612 LEU 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: 9.9990 chunk 137 optimal weight: 20.0000 chunk 79 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 105 optimal weight: 7.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN E 891 HIS ** E 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.089393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.061774 restraints weight = 83797.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.061823 restraints weight = 48320.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.062119 restraints weight = 38362.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.062070 restraints weight = 32803.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.062201 restraints weight = 30278.430| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13112 Z= 0.166 Angle : 0.638 11.011 18095 Z= 0.330 Chirality : 0.041 0.191 2071 Planarity : 0.004 0.044 2018 Dihedral : 22.070 77.688 2436 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 4.43 % Allowed : 29.20 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1379 helix: 0.83 (0.25), residues: 451 sheet: -0.82 (0.28), residues: 347 loop : -1.19 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 424 TYR 0.023 0.002 TYR E 842 PHE 0.029 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 0.00338 / 0.17 (13109) covalent geometry : angle 0.63831 / 0.33 (18089) SS BOND : bond 0.00604 / 0.31 ( 3) SS BOND : angle 0.80634 / 1.40 ( 6) hydrogen bonds : bond 0.06647 / 6.69 ( 539) hydrogen bonds : angle 5.49822 / 7.00 ( 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 130 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 76 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: 0.8530 (tmm) cc_final: 0.8201 (tmm) REVERT: C 1 MET cc_start: 0.7936 (tpp) cc_final: 0.7718 (tpp) REVERT: C 54 SER cc_start: 0.9468 (OUTLIER) cc_final: 0.8866 (m) REVERT: C 119 MET cc_start: 0.8599 (tmm) cc_final: 0.8211 (tmm) REVERT: D 1 MET cc_start: 0.8847 (tpp) cc_final: 0.8269 (tpp) REVERT: D 40 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8046 (tmm) REVERT: E 457 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: E 848 ASP cc_start: 0.9741 (m-30) cc_final: 0.9361 (p0) outliers start: 54 outliers final: 38 residues processed: 122 average time/residue: 0.0909 time to fit residues: 16.8418 Evaluate side-chains 114 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 73 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 125 GLN 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 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 78 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 97 ASP 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 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 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: 2.9990 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 146 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN ** E 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.089966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.059925 restraints weight = 82481.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061648 restraints weight = 43689.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.062929 restraints weight = 29759.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.063204 restraints weight = 23600.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.063204 restraints weight = 20842.186| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13112 Z= 0.132 Angle : 0.649 12.642 18095 Z= 0.329 Chirality : 0.042 0.283 2071 Planarity : 0.003 0.043 2018 Dihedral : 22.059 76.835 2436 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 4.02 % Allowed : 29.53 % Favored : 66.45 % 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: 0.87 (0.25), residues: 451 sheet: -0.70 (0.29), residues: 341 loop : -1.22 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 710 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 0.006 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (13109) covalent geometry : angle 0.64880 / 0.33 (18089) SS BOND : bond 0.00436 / 0.22 ( 3) SS BOND : angle 1.08043 / 1.96 ( 6) hydrogen bonds : bond 0.06336 / 6.31 ( 539) hydrogen bonds : angle 5.39216 / 6.90 ( 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 127 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 78 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: 0.8480 (tmm) cc_final: 0.8211 (tmm) REVERT: C 1 MET cc_start: 0.7936 (tpp) cc_final: 0.7718 (tpp) REVERT: C 54 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.8846 (m) REVERT: C 119 MET cc_start: 0.8616 (tmm) cc_final: 0.8229 (tmm) REVERT: C 229 MET cc_start: 0.8870 (pmt) cc_final: 0.8627 (pmt) REVERT: D 1 MET cc_start: 0.8770 (tpp) cc_final: 0.8138 (tpp) REVERT: D 40 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8112 (tmm) REVERT: D 99 LEU cc_start: 0.9372 (tp) cc_final: 0.8987 (pp) REVERT: E 457 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: E 848 ASP cc_start: 0.9765 (m-30) cc_final: 0.9466 (p0) outliers start: 49 outliers final: 35 residues processed: 122 average time/residue: 0.0838 time to fit residues: 15.5282 Evaluate side-chains 112 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 125 GLN Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 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 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 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 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: 10.0000 chunk 114 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 138 optimal weight: 30.0000 chunk 17 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN E 492 GLN ** E 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4040 r_free = 0.4040 target = 0.088676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.061764 restraints weight = 83648.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.060860 restraints weight = 50319.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.061417 restraints weight = 36448.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061453 restraints weight = 29136.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.061520 restraints weight = 28269.397| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13112 Z= 0.187 Angle : 0.677 11.813 18095 Z= 0.346 Chirality : 0.042 0.188 2071 Planarity : 0.004 0.042 2018 Dihedral : 22.106 76.059 2436 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 4.35 % Allowed : 29.20 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1379 helix: 0.88 (0.25), residues: 453 sheet: -0.88 (0.28), residues: 361 loop : -1.18 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 704 TYR 0.022 0.002 TYR E 842 PHE 0.030 0.001 PHE B 215 TRP 0.017 0.001 TRP E 707 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (13109) covalent geometry : angle 0.67620 / 0.35 (18089) SS BOND : bond 0.00701 / 0.36 ( 3) SS BOND : angle 2.00500 / 4.29 ( 6) hydrogen bonds : bond 0.06537 / 6.68 ( 539) hydrogen bonds : angle 5.43480 / 6.96 ( 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 : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: 0.8477 (tmm) cc_final: 0.8271 (tmm) REVERT: C 40 MET cc_start: 0.8739 (ttm) cc_final: 0.8514 (ttm) REVERT: C 54 SER cc_start: 0.9450 (OUTLIER) cc_final: 0.8872 (m) REVERT: C 119 MET cc_start: 0.8630 (tmm) cc_final: 0.8279 (tmm) REVERT: C 229 MET cc_start: 0.8803 (pmt) cc_final: 0.8530 (pmt) REVERT: D 1 MET cc_start: 0.8904 (tpp) cc_final: 0.8298 (tpp) REVERT: D 40 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8122 (tmm) REVERT: E 457 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: E 848 ASP cc_start: 0.9762 (m-30) cc_final: 0.9418 (p0) outliers start: 53 outliers final: 40 residues processed: 124 average time/residue: 0.0809 time to fit residues: 16.0928 Evaluate side-chains 116 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 73 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 162 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 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 102 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 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: 6.9990 chunk 19 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 0.0470 chunk 76 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.090091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.060228 restraints weight = 82243.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.061962 restraints weight = 43663.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063173 restraints weight = 29544.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.063825 restraints weight = 23278.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.064297 restraints weight = 20244.017| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13112 Z= 0.119 Angle : 0.670 13.299 18095 Z= 0.335 Chirality : 0.042 0.182 2071 Planarity : 0.003 0.042 2018 Dihedral : 22.087 74.962 2436 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 3.28 % Allowed : 30.35 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1379 helix: 0.96 (0.25), residues: 451 sheet: -0.74 (0.29), residues: 325 loop : -1.29 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 706 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 0.004 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (13109) covalent geometry : angle 0.66874 / 0.34 (18089) SS BOND : bond 0.00581 / 0.29 ( 3) SS BOND : angle 1.90745 / 3.75 ( 6) hydrogen bonds : bond 0.06069 / 6.02 ( 539) hydrogen bonds : angle 5.21504 / 6.69 ( 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 120 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 80 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.8720 (ttm) cc_final: 0.8307 (ttm) REVERT: C 54 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.8817 (m) REVERT: C 119 MET cc_start: 0.8566 (tmm) cc_final: 0.8224 (tmm) REVERT: C 229 MET cc_start: 0.8902 (pmt) cc_final: 0.8668 (pmt) REVERT: D 40 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8081 (tmm) REVERT: D 99 LEU cc_start: 0.9355 (tp) cc_final: 0.9041 (pp) REVERT: D 207 PHE cc_start: 0.8665 (m-80) cc_final: 0.8249 (m-80) REVERT: E 472 LEU cc_start: 0.9552 (tt) cc_final: 0.9329 (pp) REVERT: E 848 ASP cc_start: 0.9784 (m-30) cc_final: 0.9495 (p0) outliers start: 40 outliers final: 30 residues processed: 116 average time/residue: 0.0881 time to fit residues: 16.0966 Evaluate side-chains 109 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 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 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 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 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 879 ARG 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: 3.9990 chunk 8 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 742 HIS ** 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 = 0.4060 r_free = 0.4060 target = 0.089608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.059754 restraints weight = 82992.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.061429 restraints weight = 43900.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.062336 restraints weight = 29969.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.063193 restraints weight = 23689.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.063312 restraints weight = 20471.477| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13112 Z= 0.131 Angle : 0.693 14.522 18095 Z= 0.342 Chirality : 0.042 0.187 2071 Planarity : 0.003 0.041 2018 Dihedral : 22.004 74.236 2436 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 3.45 % Allowed : 30.60 % 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: 1.00 (0.25), residues: 453 sheet: -0.86 (0.28), residues: 347 loop : -1.24 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 547 TYR 0.021 0.001 TYR E 842 PHE 0.029 0.001 PHE B 215 TRP 0.014 0.001 TRP E 847 HIS 0.005 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (13109) covalent geometry : angle 0.69289 / 0.34 (18089) SS BOND : bond 0.00327 / 0.16 ( 3) SS BOND : angle 1.28696 / 2.69 ( 6) hydrogen bonds : bond 0.06043 / 6.08 ( 539) hydrogen bonds : angle 5.15984 / 6.63 ( 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 121 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8713 (tm-30) REVERT: C 54 SER cc_start: 0.9430 (OUTLIER) cc_final: 0.8851 (m) REVERT: C 119 MET cc_start: 0.8592 (tmm) cc_final: 0.8289 (tmm) REVERT: C 229 MET cc_start: 0.8968 (pmt) cc_final: 0.8754 (pmt) REVERT: D 1 MET cc_start: 0.8779 (tpp) cc_final: 0.8175 (tpp) REVERT: D 40 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8059 (tmm) REVERT: D 99 LEU cc_start: 0.9374 (tp) cc_final: 0.9044 (pp) REVERT: D 207 PHE cc_start: 0.8698 (m-80) cc_final: 0.8277 (m-80) REVERT: E 457 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: E 848 ASP cc_start: 0.9797 (m-30) cc_final: 0.9516 (p0) outliers start: 42 outliers final: 36 residues processed: 116 average time/residue: 0.0877 time to fit residues: 16.0374 Evaluate side-chains 117 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 7 VAL 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 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 879 ARG 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: 7.9990 chunk 85 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.088670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.062054 restraints weight = 83434.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.060932 restraints weight = 49771.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061852 restraints weight = 36417.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061513 restraints weight = 30926.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061629 restraints weight = 29100.779| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13112 Z= 0.158 Angle : 0.696 15.133 18095 Z= 0.347 Chirality : 0.041 0.169 2071 Planarity : 0.004 0.038 2018 Dihedral : 22.066 74.171 2436 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 3.36 % Allowed : 30.43 % 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: -0.66 (0.23), residues: 1379 helix: 0.97 (0.25), residues: 453 sheet: -0.83 (0.28), residues: 345 loop : -1.25 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 879 TYR 0.021 0.002 TYR E 842 PHE 0.031 0.001 PHE B 215 TRP 0.015 0.001 TRP E 847 HIS 0.005 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (13109) covalent geometry : angle 0.69549 / 0.35 (18089) SS BOND : bond 0.00300 / 0.17 ( 3) SS BOND : angle 1.42907 / 2.60 ( 6) hydrogen bonds : bond 0.06088 / 6.18 ( 539) hydrogen bonds : angle 5.21017 / 6.69 ( 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: 41 poor density : 77 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.8652 (ttm) cc_final: 0.8351 (ttm) REVERT: C 54 SER cc_start: 0.9437 (OUTLIER) cc_final: 0.8847 (m) REVERT: C 119 MET cc_start: 0.8622 (tmm) cc_final: 0.8335 (tmm) REVERT: C 199 MET cc_start: 0.8193 (tpp) cc_final: 0.7807 (tpp) REVERT: C 229 MET cc_start: 0.8901 (pmt) cc_final: 0.8657 (pmt) REVERT: D 1 MET cc_start: 0.8963 (tpp) cc_final: 0.8419 (tpp) REVERT: D 40 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8096 (tmm) REVERT: D 99 LEU cc_start: 0.9454 (tp) cc_final: 0.9119 (pp) REVERT: D 207 PHE cc_start: 0.8746 (m-80) cc_final: 0.8318 (m-80) REVERT: E 457 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: E 472 LEU cc_start: 0.9645 (pp) cc_final: 0.9435 (pp) REVERT: E 848 ASP cc_start: 0.9792 (m-30) cc_final: 0.9455 (p0) outliers start: 41 outliers final: 35 residues processed: 113 average time/residue: 0.0944 time to fit residues: 16.7938 Evaluate side-chains 114 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 167 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 7 VAL 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 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 879 ARG 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: 0.0970 chunk 14 optimal weight: 8.9990 chunk 96 optimal weight: 0.2980 chunk 3 optimal weight: 30.0000 chunk 70 optimal weight: 0.2980 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.089576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.059802 restraints weight = 82915.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061549 restraints weight = 43847.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.062480 restraints weight = 29706.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.063365 restraints weight = 23853.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.063754 restraints weight = 20862.903| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13112 Z= 0.118 Angle : 0.696 15.069 18095 Z= 0.342 Chirality : 0.042 0.202 2071 Planarity : 0.003 0.037 2018 Dihedral : 22.026 74.028 2436 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 3.28 % Allowed : 30.60 % 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: -0.62 (0.23), residues: 1379 helix: 1.03 (0.25), residues: 453 sheet: -0.79 (0.28), residues: 345 loop : -1.27 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 648 TYR 0.021 0.001 TYR E 842 PHE 0.030 0.001 PHE B 215 TRP 0.012 0.001 TRP E 847 HIS 0.004 0.001 HIS E 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (13109) covalent geometry : angle 0.69526 / 0.34 (18089) SS BOND : bond 0.00326 / 0.17 ( 3) SS BOND : angle 1.27565 / 2.25 ( 6) hydrogen bonds : bond 0.05809 / 5.76 ( 539) hydrogen bonds : angle 5.07609 / 6.53 ( 1462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.46 seconds wall clock time: 44 minutes 40.08 seconds (2680.08 seconds total)