Starting phenix.real_space_refine on Mon Jul 28 13:13:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sj7_10213/07_2025/6sj7_10213.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sj7_10213/07_2025/6sj7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6sj7_10213/07_2025/6sj7_10213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sj7_10213/07_2025/6sj7_10213.map" model { file = "/net/cci-nas-00/data/ceres_data/6sj7_10213/07_2025/6sj7_10213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sj7_10213/07_2025/6sj7_10213.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, '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: {'TYR:plan': 1, 'ARG:plan': 2} 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: 6.37, per 1000 atoms: 0.64 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.74 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: 3.97 Time building geometry restraints manager: 2.53 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- 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 : 9.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.050 0.004 TRP B1047 HIS 0.006 0.002 HIS B1140 PHE 0.042 0.003 PHE B1030 TYR 0.021 0.003 TYR B 245 ARG 0.007 0.001 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.14808 ( 345) hydrogen bonds : angle 8.13459 ( 966) SS BOND : bond 0.00707 ( 1) SS BOND : angle 0.68895 ( 2) covalent geometry : bond 0.01005 (10194) covalent geometry : angle 1.03125 (13781) *********************** 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 : 1.197 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: 0.8162 (t0) REVERT: B 787 GLU cc_start: 0.8444 (mp0) cc_final: 0.8161 (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: 0.2624 time to fit residues: 54.6006 Evaluate side-chains 114 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.117592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.095442 restraints weight = 22831.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.098403 restraints weight = 12665.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100428 restraints weight = 8640.501| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1509 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= 0.128 Angle : 0.606 7.345 13783 Z= 0.319 Chirality : 0.044 0.172 1572 Planarity : 0.005 0.053 1742 Dihedral : 6.683 50.135 1364 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.34 % Allowed : 16.14 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.22), residues: 1208 helix: -1.03 (0.42), residues: 138 sheet: -0.89 (0.25), residues: 407 loop : -2.90 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1047 HIS 0.004 0.001 HIS B 240 PHE 0.020 0.001 PHE C 259 TYR 0.012 0.001 TYR B 42 ARG 0.006 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 345) hydrogen bonds : angle 5.90176 ( 966) SS BOND : bond 0.00142 ( 1) SS BOND : angle 1.01885 ( 2) covalent geometry : bond 0.00290 (10194) covalent geometry : angle 0.60639 (13781) *********************** 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 168 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7707 (mtt90) REVERT: A 560 MET cc_start: 0.8151 (mmm) cc_final: 0.7868 (mmm) REVERT: A 575 MET cc_start: 0.7015 (mmm) cc_final: 0.6639 (mmp) REVERT: B 16 ASN cc_start: 0.8392 (t0) cc_final: 0.8113 (t0) REVERT: B 218 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6688 (ttm) REVERT: B 1129 LEU cc_start: 0.9140 (mm) cc_final: 0.8912 (mm) outliers start: 26 outliers final: 17 residues processed: 157 average time/residue: 0.2440 time to fit residues: 54.3777 Evaluate side-chains 144 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 218 MET 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 1135 GLU 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 49 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 107 optimal weight: 0.0050 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN B1106 GLN C 280 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.115302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.093330 restraints weight = 23484.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.096140 restraints weight = 13518.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098051 restraints weight = 9500.138| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10195 Z= 0.204 Angle : 0.623 6.488 13783 Z= 0.328 Chirality : 0.044 0.172 1572 Planarity : 0.004 0.041 1742 Dihedral : 6.288 55.151 1360 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.07 % Allowed : 18.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.22), residues: 1208 helix: -0.37 (0.45), residues: 139 sheet: -0.72 (0.25), residues: 404 loop : -2.70 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 562 HIS 0.004 0.001 HIS A 460 PHE 0.023 0.002 PHE B1030 TYR 0.013 0.001 TYR B 42 ARG 0.007 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 345) hydrogen bonds : angle 5.70695 ( 966) SS BOND : bond 0.00271 ( 1) SS BOND : angle 0.65892 ( 2) covalent geometry : bond 0.00468 (10194) covalent geometry : angle 0.62281 (13781) *********************** 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 152 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8413 (t0) cc_final: 0.8156 (t0) REVERT: B 318 ASP cc_start: 0.7112 (m-30) cc_final: 0.6892 (m-30) REVERT: B 714 THR cc_start: 0.8782 (m) cc_final: 0.8458 (p) outliers start: 34 outliers final: 23 residues processed: 141 average time/residue: 0.2491 time to fit residues: 50.0404 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 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 B residue 1135 GLU 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 11 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 105 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 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 = 0.3882 r_free = 0.3882 target = 0.115521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093600 restraints weight = 23336.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.096421 restraints weight = 13557.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098246 restraints weight = 9550.484| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10195 Z= 0.189 Angle : 0.623 9.137 13783 Z= 0.323 Chirality : 0.044 0.162 1572 Planarity : 0.004 0.039 1742 Dihedral : 6.049 57.984 1359 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.88 % Allowed : 19.75 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.23), residues: 1208 helix: -0.19 (0.46), residues: 139 sheet: -0.82 (0.25), residues: 419 loop : -2.57 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 562 HIS 0.005 0.001 HIS C 258 PHE 0.022 0.001 PHE B1030 TYR 0.013 0.001 TYR B 42 ARG 0.007 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 345) hydrogen bonds : angle 5.56421 ( 966) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.48424 ( 2) covalent geometry : bond 0.00433 (10194) covalent geometry : angle 0.62283 (13781) *********************** 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 162 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8430 (t0) cc_final: 0.8185 (t0) REVERT: B 209 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: B 714 THR cc_start: 0.8771 (m) cc_final: 0.8449 (p) REVERT: D 5 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7073 (tt) outliers start: 43 outliers final: 26 residues processed: 151 average time/residue: 0.2926 time to fit residues: 63.3578 Evaluate side-chains 139 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 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 929 SER Chi-restraints excluded: chain B residue 930 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN B 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.117897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.095587 restraints weight = 23171.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098618 restraints weight = 12873.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100610 restraints weight = 8850.764| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2166 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= 0.120 Angle : 0.586 10.133 13783 Z= 0.302 Chirality : 0.044 0.164 1572 Planarity : 0.004 0.036 1742 Dihedral : 5.712 59.591 1359 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.89 % Allowed : 20.92 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.23), residues: 1208 helix: 0.05 (0.46), residues: 138 sheet: -0.63 (0.25), residues: 414 loop : -2.47 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 562 HIS 0.004 0.001 HIS B 991 PHE 0.017 0.001 PHE B1030 TYR 0.009 0.001 TYR B 5 ARG 0.007 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 345) hydrogen bonds : angle 5.34147 ( 966) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.40889 ( 2) covalent geometry : bond 0.00278 (10194) covalent geometry : angle 0.58561 (13781) *********************** 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 163 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8417 (t0) cc_final: 0.8195 (t0) REVERT: B 714 THR cc_start: 0.8751 (m) cc_final: 0.8425 (p) REVERT: B 1129 LEU cc_start: 0.9073 (mm) cc_final: 0.8800 (mm) REVERT: D 5 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6996 (tt) outliers start: 32 outliers final: 22 residues processed: 154 average time/residue: 0.2266 time to fit residues: 49.6649 Evaluate side-chains 144 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 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 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 814 LEU 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 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 40 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.116582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.094443 restraints weight = 23258.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.097247 restraints weight = 13608.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.099149 restraints weight = 9587.038| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10195 Z= 0.177 Angle : 0.613 9.497 13783 Z= 0.319 Chirality : 0.044 0.157 1572 Planarity : 0.004 0.037 1742 Dihedral : 5.804 59.535 1359 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.88 % Allowed : 21.19 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.23), residues: 1208 helix: 0.09 (0.47), residues: 138 sheet: -0.64 (0.25), residues: 421 loop : -2.44 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 562 HIS 0.004 0.001 HIS C 258 PHE 0.020 0.001 PHE B1030 TYR 0.023 0.001 TYR B 726 ARG 0.008 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 345) hydrogen bonds : angle 5.40691 ( 966) SS BOND : bond 0.00503 ( 1) SS BOND : angle 1.24572 ( 2) covalent geometry : bond 0.00408 (10194) covalent geometry : angle 0.61276 (13781) *********************** 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 166 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8417 (t0) cc_final: 0.8179 (t0) REVERT: B 209 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 714 THR cc_start: 0.8757 (m) cc_final: 0.8433 (p) REVERT: B 1129 LEU cc_start: 0.9112 (mm) cc_final: 0.8865 (mm) REVERT: C 250 MET cc_start: 0.6393 (ttm) cc_final: 0.6174 (ttm) REVERT: D 5 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7036 (tt) outliers start: 43 outliers final: 28 residues processed: 156 average time/residue: 0.2266 time to fit residues: 51.2871 Evaluate side-chains 151 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 VAL 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 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 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 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 53 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 0.0010 chunk 62 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 0.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS A 268 GLN B 290 GLN C 260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.120147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097840 restraints weight = 23078.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100952 restraints weight = 12619.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102989 restraints weight = 8553.063| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10195 Z= 0.105 Angle : 0.602 10.721 13783 Z= 0.307 Chirality : 0.044 0.161 1572 Planarity : 0.004 0.035 1742 Dihedral : 5.390 56.827 1359 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.71 % Allowed : 22.54 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.23), residues: 1208 helix: 0.25 (0.47), residues: 137 sheet: -0.32 (0.26), residues: 412 loop : -2.32 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 562 HIS 0.004 0.001 HIS C 258 PHE 0.016 0.001 PHE B1030 TYR 0.018 0.001 TYR B 316 ARG 0.008 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 345) hydrogen bonds : angle 5.12767 ( 966) SS BOND : bond 0.00335 ( 1) SS BOND : angle 1.01857 ( 2) covalent geometry : bond 0.00237 (10194) covalent geometry : angle 0.60155 (13781) *********************** 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 175 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7720 (mtt180) REVERT: B 16 ASN cc_start: 0.8417 (t0) cc_final: 0.8210 (t0) REVERT: B 254 LYS cc_start: 0.8237 (pttt) cc_final: 0.7826 (ptmm) REVERT: B 714 THR cc_start: 0.8733 (m) cc_final: 0.8407 (p) REVERT: B 1129 LEU cc_start: 0.9082 (mm) cc_final: 0.8835 (mm) REVERT: B 1134 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6927 (mt-10) REVERT: D 5 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6886 (tt) outliers start: 30 outliers final: 21 residues processed: 166 average time/residue: 0.2262 time to fit residues: 53.8233 Evaluate side-chains 149 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 214 HIS 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 295 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 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 260 ASN 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 34 optimal weight: 0.0270 chunk 79 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 97 optimal weight: 0.0670 chunk 123 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 105 HIS C 280 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.120717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.098585 restraints weight = 22837.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.101679 restraints weight = 12581.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.103766 restraints weight = 8541.719| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10195 Z= 0.106 Angle : 0.602 10.556 13783 Z= 0.308 Chirality : 0.044 0.166 1572 Planarity : 0.004 0.050 1742 Dihedral : 5.232 54.059 1359 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.25 % Allowed : 24.62 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.24), residues: 1208 helix: 0.32 (0.48), residues: 137 sheet: -0.24 (0.26), residues: 405 loop : -2.22 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 562 HIS 0.004 0.001 HIS C 258 PHE 0.017 0.001 PHE B1030 TYR 0.024 0.001 TYR A 452 ARG 0.008 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 345) hydrogen bonds : angle 5.01826 ( 966) SS BOND : bond 0.00268 ( 1) SS BOND : angle 1.13923 ( 2) covalent geometry : bond 0.00246 (10194) covalent geometry : angle 0.60142 (13781) *********************** 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 160 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7754 (mtt180) REVERT: A 562 TRP cc_start: 0.7540 (m100) cc_final: 0.7268 (m100) REVERT: B 16 ASN cc_start: 0.8460 (t0) cc_final: 0.8250 (t0) REVERT: B 714 THR cc_start: 0.8711 (m) cc_final: 0.8398 (p) REVERT: B 787 GLU cc_start: 0.8119 (mp0) cc_final: 0.7820 (mp0) REVERT: B 1129 LEU cc_start: 0.9031 (mm) cc_final: 0.8780 (mm) REVERT: B 1134 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6903 (mt-10) REVERT: D 5 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6891 (tt) outliers start: 25 outliers final: 19 residues processed: 152 average time/residue: 0.2352 time to fit residues: 51.8131 Evaluate side-chains 148 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 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 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 929 SER 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 263 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 1 optimal weight: 0.0470 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN ** 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 = 0.3925 r_free = 0.3925 target = 0.118603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096342 restraints weight = 22976.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099394 restraints weight = 12740.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101448 restraints weight = 8695.127| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2761 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= 0.145 Angle : 0.618 10.354 13783 Z= 0.317 Chirality : 0.044 0.164 1572 Planarity : 0.004 0.038 1742 Dihedral : 5.345 50.072 1359 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.71 % Allowed : 24.26 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.24), residues: 1208 helix: 0.28 (0.47), residues: 137 sheet: -0.33 (0.25), residues: 423 loop : -2.24 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 562 HIS 0.005 0.001 HIS C 258 PHE 0.019 0.001 PHE B1030 TYR 0.021 0.001 TYR A 452 ARG 0.012 0.001 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 345) hydrogen bonds : angle 5.03340 ( 966) SS BOND : bond 0.00353 ( 1) SS BOND : angle 1.05742 ( 2) covalent geometry : bond 0.00340 (10194) covalent geometry : angle 0.61785 (13781) *********************** 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 155 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7680 (mtt90) REVERT: B 16 ASN cc_start: 0.8446 (t0) cc_final: 0.8232 (t0) REVERT: B 714 THR cc_start: 0.8754 (m) cc_final: 0.8441 (p) REVERT: B 787 GLU cc_start: 0.8113 (mp0) cc_final: 0.7811 (mp0) REVERT: B 1129 LEU cc_start: 0.9085 (mm) cc_final: 0.8853 (mm) REVERT: B 1134 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6915 (mt-10) REVERT: D 5 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6904 (tt) outliers start: 30 outliers final: 20 residues processed: 148 average time/residue: 0.2378 time to fit residues: 51.9908 Evaluate side-chains 144 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 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 295 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 830 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 C residue 254 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 964 ASN B 991 HIS ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.114666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092578 restraints weight = 23596.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095380 restraints weight = 13734.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097257 restraints weight = 9656.252| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10195 Z= 0.259 Angle : 0.711 9.634 13783 Z= 0.365 Chirality : 0.046 0.207 1572 Planarity : 0.004 0.038 1742 Dihedral : 5.740 31.053 1357 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.71 % Allowed : 24.53 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.23), residues: 1208 helix: 0.03 (0.47), residues: 138 sheet: -0.55 (0.25), residues: 428 loop : -2.33 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 562 HIS 0.005 0.001 HIS C 258 PHE 0.021 0.002 PHE B1030 TYR 0.019 0.002 TYR A 452 ARG 0.009 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 345) hydrogen bonds : angle 5.53456 ( 966) SS BOND : bond 0.00525 ( 1) SS BOND : angle 1.13207 ( 2) covalent geometry : bond 0.00600 (10194) covalent geometry : angle 0.71085 (13781) ********************** 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 141 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8507 (t0) cc_final: 0.8266 (t0) REVERT: B 714 THR cc_start: 0.8764 (m) cc_final: 0.8503 (p) REVERT: D 5 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6912 (tt) outliers start: 30 outliers final: 26 residues processed: 135 average time/residue: 0.3034 time to fit residues: 59.7743 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 VAL 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 295 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 830 ILE 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 991 HIS Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 100 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.118033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096233 restraints weight = 23058.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.099113 restraints weight = 13169.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.101034 restraints weight = 9189.846| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10195 Z= 0.128 Angle : 0.646 10.730 13783 Z= 0.328 Chirality : 0.045 0.176 1572 Planarity : 0.004 0.034 1742 Dihedral : 5.310 31.991 1357 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.25 % Allowed : 25.07 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1208 helix: 0.13 (0.47), residues: 138 sheet: -0.32 (0.26), residues: 412 loop : -2.23 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 562 HIS 0.008 0.001 HIS B 991 PHE 0.018 0.001 PHE B1030 TYR 0.021 0.001 TYR A 452 ARG 0.010 0.001 ARG B 989 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 345) hydrogen bonds : angle 5.25429 ( 966) SS BOND : bond 0.00269 ( 1) SS BOND : angle 1.01507 ( 2) covalent geometry : bond 0.00299 (10194) covalent geometry : angle 0.64625 (13781) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3850.24 seconds wall clock time: 71 minutes 11.49 seconds (4271.49 seconds total)