Starting phenix.real_space_refine on Wed Mar 4 03:08:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sj7_10213/03_2026/6sj7_10213.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sj7_10213/03_2026/6sj7_10213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sj7_10213/03_2026/6sj7_10213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sj7_10213/03_2026/6sj7_10213.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sj7_10213/03_2026/6sj7_10213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sj7_10213/03_2026/6sj7_10213.map" } resolution = 3.54 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 416 atoms to isotropic. 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 S 57 5.16 5 Cl 1 4.86 5 C 6393 2.51 5 N 1683 2.21 5 O 1873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10007 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2845 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 339} Chain breaks: 12 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6095 Classifications: {'peptide': 774} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 750} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 619 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 424 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'EF6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.24 Number of scatterers: 10007 At special positions: 0 Unit cell: (90.3, 95.46, 114.38, 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) Cl 1 17.00 S 57 16.00 O 1873 8.00 N 1683 7.00 C 6393 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 500.0 milliseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 29 sheets defined 11.1% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 36 through 47 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 545 through 562 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.803A pdb=" N GLN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.835A pdb=" N ALA B 760 " --> pdb=" O SER B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 990 Processing helix chain 'B' and resid 1045 through 1059 Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1101 through 1109 removed outlier: 3.634A pdb=" N VAL B1108 " --> pdb=" O LYS B1104 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B1109 " --> pdb=" O MET B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1137 Processing helix chain 'C' and resid 262 through 271 removed outlier: 3.536A pdb=" N LEU C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 302 through 311 removed outlier: 3.824A pdb=" N GLU C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.501A pdb=" N VAL A 61 " --> pdb=" O TRP A 597 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 83 removed outlier: 6.818A pdb=" N LEU A 91 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE A 83 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TYR A 89 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 109 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 125 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP A 111 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 470 through 471 removed outlier: 4.009A pdb=" N SER A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 482 removed outlier: 6.095A pdb=" N ILE A 476 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY A 493 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE A 478 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN A 491 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 480 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA A 520 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL A 531 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP A 522 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 529 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 3.730A pdb=" N VAL B1006 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 21 Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 21 Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 67 removed outlier: 4.278A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N GLN D 45 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ARG B 103 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE D 47 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N HIS B 105 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR D 49 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N ASN B 107 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS B 153 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.676A pdb=" N SER B 94 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.623A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.623A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 221 Processing sheet with id=AB6, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.656A pdb=" N GLY B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 272 " --> pdb=" O HIS B 261 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ARG B 263 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ARG B 270 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 275 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 287 through 288 Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.661A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 313 removed outlier: 6.051A pdb=" N SER B 331 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 352 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 362 through 365 removed outlier: 3.745A pdb=" N CYS B 363 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 376 " --> pdb=" O CYS B 363 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 365 " --> pdb=" O GLN B 374 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.722A pdb=" N SER B 738 " --> pdb=" O PRO B 721 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS B 723 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 742 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR B 750 " --> pdb=" O VAL B 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.722A pdb=" N SER B 738 " --> pdb=" O PRO B 721 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS B 723 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS B 803 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP B 795 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 801 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 762 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 804 " --> pdb=" O SER B 762 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 811 through 819 removed outlier: 5.168A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 815 " --> pdb=" O GLY B 832 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN B 845 " --> pdb=" O MET B 835 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY B 846 " --> pdb=" O GLU B 865 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU B 865 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 848 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B 863 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 850 " --> pdb=" O VAL B 861 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 872 through 875 removed outlier: 3.775A pdb=" N SER B 872 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 888 " --> pdb=" O ASN B 904 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN B 904 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 911 through 917 removed outlier: 3.811A pdb=" N TYR B 913 " --> pdb=" O GLY B 924 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 917 " --> pdb=" O PHE B 920 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 920 " --> pdb=" O LYS B 917 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA B 946 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 954 through 959 removed outlier: 3.975A pdb=" N ASN B 973 " --> pdb=" O GLU B 969 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1076 through 1077 Processing sheet with id=AC9, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AD1, first strand: chain 'C' and resid 283 through 284 removed outlier: 3.589A pdb=" N ARG C 289 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 314 through 316 371 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.09 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: 3223 1.34 - 1.46: 2370 1.46 - 1.59: 4512 1.59 - 1.71: 2 1.71 - 1.83: 87 Bond restraints: 10194 Sorted by residual: bond pdb=" CA HIS A 214 " pdb=" CB HIS A 214 " ideal model delta sigma weight residual 1.526 1.455 0.071 1.51e-02 4.39e+03 2.19e+01 bond pdb=" C4 EF6 A 701 " pdb=" N1 EF6 A 701 " ideal model delta sigma weight residual 1.376 1.307 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C GLU B 54 " pdb=" N VAL B 55 " ideal model delta sigma weight residual 1.329 1.279 0.049 1.69e-02 3.50e+03 8.52e+00 bond pdb=" C2 EF6 A 701 " pdb=" C3 EF6 A 701 " ideal model delta sigma weight residual 1.431 1.489 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" N ARG B 928 " pdb=" CA ARG B 928 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.18e-02 7.18e+03 7.19e+00 ... (remaining 10189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12886 1.90 - 3.80: 756 3.80 - 5.69: 107 5.69 - 7.59: 22 7.59 - 9.49: 10 Bond angle restraints: 13781 Sorted by residual: angle pdb=" N VAL A 36 " pdb=" CA VAL A 36 " pdb=" C VAL A 36 " ideal model delta sigma weight residual 112.96 107.94 5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" C ILE B 884 " pdb=" N ASN B 885 " pdb=" CA ASN B 885 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C THR A 247 " pdb=" N SER A 248 " pdb=" CA SER A 248 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLU B 289 " pdb=" N GLN B 290 " pdb=" CA GLN B 290 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C GLN A 130 " pdb=" N ASP A 131 " pdb=" CA ASP A 131 " ideal model delta sigma weight residual 122.46 127.60 -5.14 1.41e+00 5.03e-01 1.33e+01 ... (remaining 13776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 5297 18.09 - 36.18: 646 36.18 - 54.27: 114 54.27 - 72.37: 27 72.37 - 90.46: 11 Dihedral angle restraints: 6095 sinusoidal: 2453 harmonic: 3642 Sorted by residual: dihedral pdb=" CA GLU C 271 " pdb=" C GLU C 271 " pdb=" N PRO C 272 " pdb=" CA PRO C 272 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LEU C 316 " pdb=" C LEU C 316 " pdb=" N ALA C 317 " pdb=" CA ALA C 317 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PRO B 225 " pdb=" C PRO B 225 " pdb=" N PHE B 226 " pdb=" CA PHE B 226 " ideal model delta harmonic sigma weight residual 180.00 152.98 27.02 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 6092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1083 0.055 - 0.111: 373 0.111 - 0.166: 94 0.166 - 0.222: 17 0.222 - 0.277: 5 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CB VAL B1033 " pdb=" CA VAL B1033 " pdb=" CG1 VAL B1033 " pdb=" CG2 VAL B1033 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE B 390 " pdb=" CA ILE B 390 " pdb=" CG1 ILE B 390 " pdb=" CG2 ILE B 390 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR A 141 " pdb=" CA THR A 141 " pdb=" OG1 THR A 141 " pdb=" CG2 THR A 141 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1569 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 316 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C LEU C 316 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU C 316 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 317 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1047 " 0.024 2.00e-02 2.50e+03 1.85e-02 8.54e+00 pdb=" CG TRP B1047 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B1047 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B1047 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1047 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1047 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1047 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1047 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1047 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B1047 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 731 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" CD GLN B 731 " -0.046 2.00e-02 2.50e+03 pdb=" OE1 GLN B 731 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN B 731 " 0.015 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2777 2.80 - 3.33: 8707 3.33 - 3.85: 16464 3.85 - 4.38: 18689 4.38 - 4.90: 33004 Nonbonded interactions: 79641 Sorted by model distance: nonbonded pdb=" OH TYR B 726 " pdb=" OE1 GLN B 796 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR B 13 " pdb=" OD1 ASN B 355 " model vdw 2.285 3.040 nonbonded pdb=" OG SER B 872 " pdb=" O LEU B 912 " model vdw 2.286 3.040 nonbonded pdb=" OG SER B 883 " pdb=" O ALA B 911 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 94 " pdb=" OG SER B 97 " model vdw 2.292 3.040 ... (remaining 79636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.010 0.071 10195 Z= 0.446 Angle : 1.031 9.490 13783 Z= 0.564 Chirality : 0.060 0.277 1572 Planarity : 0.006 0.062 1742 Dihedral : 16.416 90.457 3732 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.26 % Favored : 88.66 % Rotamer: Outliers : 0.81 % Allowed : 13.53 % Favored : 85.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.38 % 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: -3.72 (0.20), residues: 1208 helix: -2.78 (0.32), residues: 134 sheet: -1.27 (0.23), residues: 437 loop : -3.38 (0.19), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 111 TYR 0.021 0.003 TYR B 245 PHE 0.042 0.003 PHE B1030 TRP 0.050 0.004 TRP B1047 HIS 0.006 0.002 HIS B1140 Details of bonding type rmsd covalent geometry : bond 0.01005 (10194) covalent geometry : angle 1.03125 (13781) SS BOND : bond 0.00707 ( 1) SS BOND : angle 0.68895 ( 2) hydrogen bonds : bond 0.14808 ( 345) hydrogen bonds : angle 8.13459 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 MET cc_start: 0.8151 (mmm) cc_final: 0.7796 (mmm) REVERT: B 16 ASN cc_start: 0.8480 (t0) cc_final: 0.8163 (t0) REVERT: B 787 GLU cc_start: 0.8444 (mp0) cc_final: 0.8162 (mp0) REVERT: B 958 GLU cc_start: 0.7727 (tp30) cc_final: 0.7334 (tp30) outliers start: 9 outliers final: 4 residues processed: 154 average time/residue: 0.1199 time to fit residues: 24.8595 Evaluate side-chains 115 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 36 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN B 4 ASN B 261 HIS B 262 ASN B1034 ASN C 260 ASN C 280 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.118248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.096096 restraints weight = 23009.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.099128 restraints weight = 12794.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101147 restraints weight = 8730.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102450 restraints weight = 6792.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.103055 restraints weight = 5744.471| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10195 Z= 0.120 Angle : 0.597 7.457 13783 Z= 0.313 Chirality : 0.044 0.169 1572 Planarity : 0.004 0.053 1742 Dihedral : 6.580 50.498 1364 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.25 % Allowed : 15.87 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.22), residues: 1208 helix: -0.99 (0.42), residues: 138 sheet: -0.84 (0.25), residues: 401 loop : -2.88 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.011 0.001 TYR B 42 PHE 0.020 0.001 PHE C 259 TRP 0.015 0.001 TRP B1047 HIS 0.004 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00269 (10194) covalent geometry : angle 0.59675 (13781) SS BOND : bond 0.00154 ( 1) SS BOND : angle 1.06058 ( 2) hydrogen bonds : bond 0.03413 ( 345) hydrogen bonds : angle 5.80056 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.400 Fit side-chains REVERT: A 42 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7707 (mtt90) REVERT: A 560 MET cc_start: 0.8130 (mmm) cc_final: 0.7799 (mmm) REVERT: A 575 MET cc_start: 0.6988 (mmm) cc_final: 0.6503 (mmp) REVERT: B 16 ASN cc_start: 0.8354 (t0) cc_final: 0.8070 (t0) REVERT: B 1129 LEU cc_start: 0.9119 (mm) cc_final: 0.8918 (mm) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 0.0973 time to fit residues: 21.7424 Evaluate side-chains 142 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 810 ASN B1106 GLN C 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.117108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094870 restraints weight = 23378.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097908 restraints weight = 12865.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099909 restraints weight = 8758.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101212 restraints weight = 6833.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.101968 restraints weight = 5784.510| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10195 Z= 0.148 Angle : 0.590 6.686 13783 Z= 0.310 Chirality : 0.044 0.167 1572 Planarity : 0.004 0.040 1742 Dihedral : 6.040 53.190 1360 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.71 % Allowed : 18.49 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.22), residues: 1208 helix: -0.26 (0.45), residues: 139 sheet: -0.63 (0.25), residues: 404 loop : -2.65 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.010 0.001 TYR A 139 PHE 0.021 0.001 PHE C 259 TRP 0.014 0.001 TRP A 562 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00337 (10194) covalent geometry : angle 0.58993 (13781) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.56309 ( 2) hydrogen bonds : bond 0.03312 ( 345) hydrogen bonds : angle 5.51476 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7663 (mtt90) REVERT: B 16 ASN cc_start: 0.8469 (t0) cc_final: 0.8197 (t0) REVERT: B 714 THR cc_start: 0.8864 (m) cc_final: 0.8536 (p) outliers start: 30 outliers final: 19 residues processed: 151 average time/residue: 0.1065 time to fit residues: 22.4512 Evaluate side-chains 140 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 0.0870 chunk 2 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN B 991 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.119276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096934 restraints weight = 23509.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100095 restraints weight = 12899.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.102168 restraints weight = 8728.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103516 restraints weight = 6740.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104293 restraints weight = 5692.980| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10195 Z= 0.107 Angle : 0.564 7.018 13783 Z= 0.295 Chirality : 0.044 0.160 1572 Planarity : 0.004 0.055 1742 Dihedral : 5.559 54.394 1359 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.80 % Allowed : 19.39 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1208 helix: 0.01 (0.46), residues: 139 sheet: -0.49 (0.25), residues: 407 loop : -2.51 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.008 0.001 TYR B 5 PHE 0.018 0.001 PHE C 259 TRP 0.012 0.001 TRP A 562 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00243 (10194) covalent geometry : angle 0.56349 (13781) SS BOND : bond 0.00379 ( 1) SS BOND : angle 1.21493 ( 2) hydrogen bonds : bond 0.03054 ( 345) hydrogen bonds : angle 5.25475 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7645 (mtt90) REVERT: A 180 ILE cc_start: 0.7809 (mm) cc_final: 0.7603 (mt) REVERT: B 16 ASN cc_start: 0.8479 (t0) cc_final: 0.8233 (t0) REVERT: B 714 THR cc_start: 0.8834 (m) cc_final: 0.8505 (p) outliers start: 31 outliers final: 20 residues processed: 159 average time/residue: 0.1006 time to fit residues: 22.7428 Evaluate side-chains 145 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.117939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095881 restraints weight = 22973.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.098744 restraints weight = 13408.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.100541 restraints weight = 9435.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101864 restraints weight = 7530.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102708 restraints weight = 6431.148| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10195 Z= 0.132 Angle : 0.568 6.936 13783 Z= 0.297 Chirality : 0.043 0.155 1572 Planarity : 0.003 0.037 1742 Dihedral : 5.542 55.567 1359 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.25 % Allowed : 20.65 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.23), residues: 1208 helix: 0.21 (0.47), residues: 138 sheet: -0.38 (0.26), residues: 406 loop : -2.42 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.018 0.001 TYR B 726 PHE 0.019 0.001 PHE B1030 TRP 0.013 0.001 TRP A 562 HIS 0.005 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00305 (10194) covalent geometry : angle 0.56757 (13781) SS BOND : bond 0.00374 ( 1) SS BOND : angle 1.10196 ( 2) hydrogen bonds : bond 0.03039 ( 345) hydrogen bonds : angle 5.19627 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7536 (mtm-85) REVERT: A 219 HIS cc_start: 0.6199 (p-80) cc_final: 0.5689 (p-80) REVERT: B 16 ASN cc_start: 0.8452 (t0) cc_final: 0.8229 (t0) REVERT: B 714 THR cc_start: 0.8742 (m) cc_final: 0.8412 (p) REVERT: B 1129 LEU cc_start: 0.9054 (mm) cc_final: 0.8769 (mm) REVERT: C 261 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6852 (mm) REVERT: D 5 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6915 (tt) outliers start: 36 outliers final: 24 residues processed: 159 average time/residue: 0.0943 time to fit residues: 21.5426 Evaluate side-chains 146 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.118463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096437 restraints weight = 23316.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.099239 restraints weight = 13467.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.101201 restraints weight = 9452.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102521 restraints weight = 7455.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.103394 restraints weight = 6329.998| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10195 Z= 0.138 Angle : 0.574 7.490 13783 Z= 0.298 Chirality : 0.043 0.154 1572 Planarity : 0.003 0.036 1742 Dihedral : 5.513 57.090 1359 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.43 % Allowed : 21.46 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.23), residues: 1208 helix: 0.26 (0.47), residues: 138 sheet: -0.39 (0.25), residues: 418 loop : -2.35 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 18 TYR 0.012 0.001 TYR B 316 PHE 0.018 0.001 PHE B1030 TRP 0.017 0.001 TRP A 562 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00318 (10194) covalent geometry : angle 0.57368 (13781) SS BOND : bond 0.00362 ( 1) SS BOND : angle 1.06413 ( 2) hydrogen bonds : bond 0.03097 ( 345) hydrogen bonds : angle 5.14543 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7487 (mtm-85) REVERT: B 16 ASN cc_start: 0.8384 (t0) cc_final: 0.8182 (t0) REVERT: B 714 THR cc_start: 0.8736 (m) cc_final: 0.8416 (p) REVERT: D 5 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6897 (tt) outliers start: 38 outliers final: 28 residues processed: 152 average time/residue: 0.0943 time to fit residues: 20.3570 Evaluate side-chains 150 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.118570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096683 restraints weight = 23104.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.099536 restraints weight = 13327.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.101454 restraints weight = 9346.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102782 restraints weight = 7363.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103618 restraints weight = 6226.925| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10195 Z= 0.130 Angle : 0.568 7.641 13783 Z= 0.295 Chirality : 0.043 0.154 1572 Planarity : 0.003 0.036 1742 Dihedral : 5.463 59.083 1359 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.43 % Allowed : 22.00 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.23), residues: 1208 helix: 0.31 (0.47), residues: 138 sheet: -0.32 (0.25), residues: 418 loop : -2.30 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 18 TYR 0.012 0.001 TYR B 316 PHE 0.018 0.001 PHE B1030 TRP 0.016 0.001 TRP A 562 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00300 (10194) covalent geometry : angle 0.56797 (13781) SS BOND : bond 0.00318 ( 1) SS BOND : angle 0.98138 ( 2) hydrogen bonds : bond 0.03061 ( 345) hydrogen bonds : angle 5.08093 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7487 (mtm-85) REVERT: B 16 ASN cc_start: 0.8390 (t0) cc_final: 0.8167 (t0) REVERT: B 714 THR cc_start: 0.8736 (m) cc_final: 0.8436 (p) REVERT: B 1129 LEU cc_start: 0.8979 (mm) cc_final: 0.8721 (mm) REVERT: B 1134 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6838 (mt-10) REVERT: D 5 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6856 (tt) outliers start: 38 outliers final: 28 residues processed: 156 average time/residue: 0.0929 time to fit residues: 20.7912 Evaluate side-chains 151 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.117485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.095540 restraints weight = 23099.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098349 restraints weight = 13354.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.100221 restraints weight = 9408.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101443 restraints weight = 7465.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.102271 restraints weight = 6387.860| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10195 Z= 0.164 Angle : 0.608 8.749 13783 Z= 0.316 Chirality : 0.044 0.151 1572 Planarity : 0.004 0.036 1742 Dihedral : 5.573 59.660 1359 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.34 % Allowed : 22.54 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.23), residues: 1208 helix: 0.29 (0.47), residues: 138 sheet: -0.34 (0.25), residues: 419 loop : -2.29 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 251 TYR 0.012 0.001 TYR B 42 PHE 0.020 0.001 PHE B1030 TRP 0.022 0.001 TRP A 562 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00378 (10194) covalent geometry : angle 0.60765 (13781) SS BOND : bond 0.00339 ( 1) SS BOND : angle 0.91258 ( 2) hydrogen bonds : bond 0.03197 ( 345) hydrogen bonds : angle 5.18853 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7539 (mtm-85) REVERT: B 16 ASN cc_start: 0.8419 (t0) cc_final: 0.8201 (t0) REVERT: B 254 LYS cc_start: 0.8147 (pttt) cc_final: 0.7870 (ptmm) REVERT: B 714 THR cc_start: 0.8750 (m) cc_final: 0.8468 (p) REVERT: B 1129 LEU cc_start: 0.9078 (mm) cc_final: 0.8800 (mm) REVERT: D 5 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6851 (tt) outliers start: 37 outliers final: 30 residues processed: 145 average time/residue: 0.0914 time to fit residues: 19.3606 Evaluate side-chains 149 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 0.0980 chunk 7 optimal weight: 0.0980 chunk 122 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.119140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.097244 restraints weight = 22897.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100122 restraints weight = 13171.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102038 restraints weight = 9210.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.103311 restraints weight = 7287.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104061 restraints weight = 6206.019| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10195 Z= 0.110 Angle : 0.598 11.549 13783 Z= 0.308 Chirality : 0.043 0.153 1572 Planarity : 0.003 0.035 1742 Dihedral : 5.306 57.054 1359 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.80 % Allowed : 22.99 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.24), residues: 1208 helix: 0.28 (0.47), residues: 137 sheet: -0.27 (0.26), residues: 412 loop : -2.20 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 18 TYR 0.011 0.001 TYR B 316 PHE 0.018 0.001 PHE B1030 TRP 0.020 0.001 TRP A 562 HIS 0.006 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00253 (10194) covalent geometry : angle 0.59814 (13781) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.78186 ( 2) hydrogen bonds : bond 0.03061 ( 345) hydrogen bonds : angle 5.10155 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.338 Fit side-chains REVERT: A 42 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7491 (mtm-85) REVERT: B 16 ASN cc_start: 0.8380 (t0) cc_final: 0.8176 (t0) REVERT: B 714 THR cc_start: 0.8719 (m) cc_final: 0.8429 (p) REVERT: B 1129 LEU cc_start: 0.9055 (mm) cc_final: 0.8816 (mm) REVERT: B 1134 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6929 (mt-10) REVERT: D 5 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6751 (tt) outliers start: 31 outliers final: 28 residues processed: 159 average time/residue: 0.0901 time to fit residues: 20.8371 Evaluate side-chains 154 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN B 290 GLN B 964 ASN ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.114995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092918 restraints weight = 23343.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095683 restraints weight = 13654.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097564 restraints weight = 9664.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.098754 restraints weight = 7677.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.099492 restraints weight = 6607.599| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10195 Z= 0.270 Angle : 0.713 10.483 13783 Z= 0.367 Chirality : 0.046 0.168 1572 Planarity : 0.004 0.038 1742 Dihedral : 5.880 55.082 1359 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.34 % Allowed : 23.08 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.23), residues: 1208 helix: 0.01 (0.46), residues: 137 sheet: -0.47 (0.25), residues: 421 loop : -2.32 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 18 TYR 0.036 0.002 TYR B 316 PHE 0.023 0.002 PHE B1030 TRP 0.047 0.003 TRP A 562 HIS 0.008 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00622 (10194) covalent geometry : angle 0.71331 (13781) SS BOND : bond 0.00509 ( 1) SS BOND : angle 1.00779 ( 2) hydrogen bonds : bond 0.03683 ( 345) hydrogen bonds : angle 5.55742 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.402 Fit side-chains REVERT: A 42 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7569 (mtm-85) REVERT: B 16 ASN cc_start: 0.8515 (t0) cc_final: 0.8272 (t0) REVERT: B 209 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: B 714 THR cc_start: 0.8790 (m) cc_final: 0.8537 (p) REVERT: D 5 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6815 (tt) outliers start: 37 outliers final: 32 residues processed: 141 average time/residue: 0.0884 time to fit residues: 18.1981 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 116 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** C 258 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 = 0.3901 r_free = 0.3901 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094944 restraints weight = 23291.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.097813 restraints weight = 13466.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.099675 restraints weight = 9460.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.100782 restraints weight = 7527.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101690 restraints weight = 6494.791| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10195 Z= 0.172 Angle : 0.668 11.616 13783 Z= 0.341 Chirality : 0.045 0.200 1572 Planarity : 0.004 0.036 1742 Dihedral : 5.626 49.671 1359 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.16 % Allowed : 23.99 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.23), residues: 1208 helix: 0.01 (0.46), residues: 138 sheet: -0.31 (0.25), residues: 406 loop : -2.27 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 18 TYR 0.018 0.001 TYR A 452 PHE 0.020 0.001 PHE B1030 TRP 0.057 0.002 TRP A 562 HIS 0.012 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00397 (10194) covalent geometry : angle 0.66794 (13781) SS BOND : bond 0.00307 ( 1) SS BOND : angle 0.87019 ( 2) hydrogen bonds : bond 0.03429 ( 345) hydrogen bonds : angle 5.42730 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1641.22 seconds wall clock time: 29 minutes 6.41 seconds (1746.41 seconds total)