Starting phenix.real_space_refine on Fri Feb 14 15:59:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sj7_10213/02_2025/6sj7_10213.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sj7_10213/02_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_10213/02_2025/6sj7_10213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sj7_10213/02_2025/6sj7_10213.map" model { file = "/net/cci-nas-00/data/ceres_data/6sj7_10213/02_2025/6sj7_10213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sj7_10213/02_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.15, per 1000 atoms: 0.61 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: 2.13 Conformation dependent library (CDL) restraints added in 1.3 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: 1.65 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: 4.44 Time building geometry restraints manager: 2.47 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.100 Process input model: 26.360 Find NCS groups from input model: 0.110 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.500 ------------------------------------------------------------------------------- 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 10194 Z= 0.654 Angle : 1.031 9.490 13781 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 *********************** 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 : 1.143 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: 0.2690 time to fit residues: 55.7309 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 : 1.171 ------------------------------------------------------------------------------- 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 = 0.117591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095425 restraints weight = 22833.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.098462 restraints weight = 12606.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100502 restraints weight = 8583.327| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 10194 Z= 0.183 Angle : 0.606 7.345 13781 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 *********************** 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 : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7707 (mtt90) REVERT: A 560 MET cc_start: 0.8152 (mmm) cc_final: 0.7869 (mmm) REVERT: A 575 MET cc_start: 0.7015 (mmm) cc_final: 0.6638 (mmp) REVERT: B 16 ASN cc_start: 0.8390 (t0) cc_final: 0.8111 (t0) REVERT: B 218 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6687 (ttm) REVERT: B 1129 LEU cc_start: 0.9139 (mm) cc_final: 0.8913 (mm) outliers start: 26 outliers final: 17 residues processed: 157 average time/residue: 0.2340 time to fit residues: 51.8009 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 : 1.169 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN B 290 GLN B 964 ASN B1106 GLN C 280 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.113902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091833 restraints weight = 23727.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094601 restraints weight = 13850.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.096417 restraints weight = 9764.080| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10194 Z= 0.386 Angle : 0.675 7.126 13781 Z= 0.354 Chirality : 0.045 0.178 1572 Planarity : 0.005 0.042 1742 Dihedral : 6.543 56.259 1360 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.34 % Allowed : 18.85 % 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 (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: -2.62 (0.22), residues: 1208 helix: -0.46 (0.45), residues: 141 sheet: -0.79 (0.25), residues: 404 loop : -2.76 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 562 HIS 0.005 0.001 HIS A 460 PHE 0.028 0.002 PHE B1030 TYR 0.015 0.002 TYR B 42 ARG 0.007 0.001 ARG D 18 *********************** 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 147 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8454 (t0) cc_final: 0.8177 (t0) REVERT: B 209 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: B 714 THR cc_start: 0.8823 (m) cc_final: 0.8510 (p) REVERT: D 5 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7046 (tt) outliers start: 37 outliers final: 24 residues processed: 136 average time/residue: 0.2414 time to fit residues: 46.3339 Evaluate side-chains 128 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 453 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 105 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.116779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094918 restraints weight = 23221.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097757 restraints weight = 13372.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.099625 restraints weight = 9364.790| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10194 Z= 0.205 Angle : 0.605 10.270 13781 Z= 0.311 Chirality : 0.044 0.163 1572 Planarity : 0.004 0.038 1742 Dihedral : 5.944 58.573 1360 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.61 % Allowed : 19.84 % Favored : 76.56 % 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: -2.33 (0.23), residues: 1208 helix: -0.11 (0.46), residues: 139 sheet: -0.62 (0.25), residues: 406 loop : -2.58 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 562 HIS 0.004 0.001 HIS C 258 PHE 0.018 0.001 PHE B1030 TYR 0.010 0.001 TYR B 5 ARG 0.007 0.000 ARG D 18 *********************** 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 166 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8396 (t0) cc_final: 0.8173 (t0) REVERT: B 714 THR cc_start: 0.8748 (m) cc_final: 0.8420 (p) outliers start: 40 outliers final: 25 residues processed: 156 average time/residue: 0.2331 time to fit residues: 51.1579 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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 848 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN B 991 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.118302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096288 restraints weight = 23194.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.099177 restraints weight = 13337.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.101098 restraints weight = 9344.101| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10194 Z= 0.177 Angle : 0.580 9.814 13781 Z= 0.301 Chirality : 0.043 0.154 1572 Planarity : 0.004 0.037 1742 Dihedral : 5.682 59.422 1360 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.98 % Allowed : 20.56 % Favored : 76.47 % 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: -2.15 (0.23), residues: 1208 helix: 0.06 (0.46), residues: 138 sheet: -0.51 (0.25), residues: 428 loop : -2.51 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 562 HIS 0.003 0.001 HIS C 258 PHE 0.017 0.001 PHE B1030 TYR 0.023 0.001 TYR B 726 ARG 0.008 0.000 ARG D 18 *********************** 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 158 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7747 (mtt180) REVERT: A 560 MET cc_start: 0.8294 (mmm) cc_final: 0.8034 (mmm) REVERT: B 16 ASN cc_start: 0.8379 (t0) cc_final: 0.8170 (t0) REVERT: B 714 THR cc_start: 0.8717 (m) cc_final: 0.8397 (p) REVERT: B 1129 LEU cc_start: 0.9101 (mm) cc_final: 0.8827 (mm) outliers start: 33 outliers final: 24 residues processed: 149 average time/residue: 0.2277 time to fit residues: 48.1915 Evaluate side-chains 143 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 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 848 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN C 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.115863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094490 restraints weight = 23346.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.097032 restraints weight = 13592.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097819 restraints weight = 9510.032| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10194 Z= 0.299 Angle : 0.620 9.337 13781 Z= 0.323 Chirality : 0.044 0.158 1572 Planarity : 0.004 0.057 1742 Dihedral : 5.794 58.631 1359 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.97 % Allowed : 21.01 % Favored : 75.02 % 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: -2.16 (0.23), residues: 1208 helix: 0.15 (0.47), residues: 138 sheet: -0.64 (0.25), residues: 421 loop : -2.43 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 562 HIS 0.006 0.001 HIS B 991 PHE 0.022 0.001 PHE B1030 TYR 0.014 0.001 TYR B 42 ARG 0.008 0.000 ARG D 18 *********************** 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: 44 poor density : 119 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8475 (t0) cc_final: 0.8232 (t0) REVERT: B 714 THR cc_start: 0.8746 (m) cc_final: 0.8425 (p) REVERT: B 910 MET cc_start: 0.7271 (tpt) cc_final: 0.7060 (tpp) REVERT: B 1129 LEU cc_start: 0.9101 (mm) cc_final: 0.8879 (mm) REVERT: D 5 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7000 (tt) outliers start: 44 outliers final: 36 residues processed: 150 average time/residue: 0.2141 time to fit residues: 46.1946 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 : 1.235 ------------------------------------------------------------------------------- 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 A residue 559 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 219 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 848 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 260 ASN Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 266 LEU 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: 0.3980 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 14 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 290 GLN C 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.119123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.097174 restraints weight = 23246.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.100089 restraints weight = 13267.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.102026 restraints weight = 9249.682| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10194 Z= 0.154 Angle : 0.594 10.499 13781 Z= 0.305 Chirality : 0.043 0.148 1572 Planarity : 0.004 0.035 1742 Dihedral : 5.401 55.794 1359 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % 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 (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: -1.91 (0.24), residues: 1208 helix: 0.30 (0.47), residues: 137 sheet: -0.29 (0.25), residues: 422 loop : -2.40 (0.22), residues: 649 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 0.010 0.001 TYR B 726 ARG 0.008 0.000 ARG D 18 *********************** 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 171 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7729 (mtt180) REVERT: B 16 ASN cc_start: 0.8386 (t0) cc_final: 0.8177 (t0) REVERT: B 254 LYS cc_start: 0.8192 (pttt) cc_final: 0.7862 (ptmm) REVERT: B 714 THR cc_start: 0.8688 (m) cc_final: 0.8369 (p) REVERT: B 1129 LEU cc_start: 0.9074 (mm) cc_final: 0.8844 (mm) REVERT: B 1134 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6792 (mt-10) outliers start: 37 outliers final: 29 residues processed: 159 average time/residue: 0.2182 time to fit residues: 50.1366 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 : 1.115 ------------------------------------------------------------------------------- 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 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 219 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 848 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 1065 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 296 ILE 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: 0.0170 chunk 79 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 71 optimal weight: 0.0020 overall best weight: 0.5828 ------------------------------------------------------------------------------- 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 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.118831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096908 restraints weight = 22972.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.099813 restraints weight = 13292.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.101762 restraints weight = 9290.829| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10194 Z= 0.162 Angle : 0.591 10.617 13781 Z= 0.305 Chirality : 0.044 0.164 1572 Planarity : 0.003 0.035 1742 Dihedral : 5.299 52.122 1359 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.98 % Allowed : 23.17 % Favored : 73.85 % 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: -1.79 (0.24), residues: 1208 helix: 0.32 (0.47), residues: 137 sheet: -0.22 (0.26), residues: 412 loop : -2.26 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 562 HIS 0.006 0.001 HIS A 177 PHE 0.020 0.001 PHE A 157 TYR 0.009 0.001 TYR A 181 ARG 0.008 0.000 ARG D 18 *********************** 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 165 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7760 (mtt180) REVERT: B 254 LYS cc_start: 0.8173 (pttt) cc_final: 0.7885 (ptmm) REVERT: B 714 THR cc_start: 0.8679 (m) cc_final: 0.8368 (p) REVERT: B 1129 LEU cc_start: 0.9066 (mm) cc_final: 0.8822 (mm) REVERT: B 1134 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6772 (mt-10) REVERT: D 5 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6899 (tt) outliers start: 33 outliers final: 25 residues processed: 154 average time/residue: 0.2337 time to fit residues: 50.9817 Evaluate side-chains 149 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 123 ILE 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 848 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 LEU 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 265 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 296 ILE 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 77 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 0.0370 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.119468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.097697 restraints weight = 22812.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.100625 restraints weight = 13086.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102580 restraints weight = 9074.124| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10194 Z= 0.165 Angle : 0.607 10.943 13781 Z= 0.309 Chirality : 0.044 0.162 1572 Planarity : 0.003 0.035 1742 Dihedral : 5.173 45.268 1359 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.98 % Allowed : 23.99 % 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: -1.71 (0.24), residues: 1208 helix: 0.33 (0.47), residues: 137 sheet: -0.18 (0.25), residues: 418 loop : -2.21 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 562 HIS 0.007 0.001 HIS C 258 PHE 0.018 0.001 PHE B1030 TYR 0.024 0.001 TYR A 452 ARG 0.008 0.000 ARG D 18 *********************** 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 157 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7762 (mtt180) REVERT: B 714 THR cc_start: 0.8663 (m) cc_final: 0.8377 (p) REVERT: B 1129 LEU cc_start: 0.9043 (mm) cc_final: 0.8795 (mm) REVERT: B 1134 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6825 (mt-10) REVERT: D 5 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6880 (tt) outliers start: 33 outliers final: 30 residues processed: 147 average time/residue: 0.2242 time to fit residues: 47.3020 Evaluate side-chains 153 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 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 123 ILE 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 848 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 1065 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 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 120 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.118546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096734 restraints weight = 23106.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099642 restraints weight = 13211.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.101578 restraints weight = 9159.493| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10194 Z= 0.189 Angle : 0.612 10.633 13781 Z= 0.312 Chirality : 0.044 0.164 1572 Planarity : 0.004 0.036 1742 Dihedral : 5.020 31.780 1357 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.07 % Allowed : 24.17 % 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: -1.71 (0.24), residues: 1208 helix: 0.31 (0.47), residues: 137 sheet: -0.24 (0.25), residues: 428 loop : -2.17 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 562 HIS 0.006 0.001 HIS C 258 PHE 0.021 0.001 PHE C 270 TYR 0.022 0.001 TYR A 452 ARG 0.008 0.000 ARG D 18 ********************** 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 157 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7679 (mtt90) REVERT: B 714 THR cc_start: 0.8676 (m) cc_final: 0.8401 (p) REVERT: B 1129 LEU cc_start: 0.9043 (mm) cc_final: 0.8806 (mm) REVERT: B 1134 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6840 (mt-10) REVERT: D 5 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6749 (tt) outliers start: 34 outliers final: 31 residues processed: 148 average time/residue: 0.2279 time to fit residues: 48.6226 Evaluate side-chains 154 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU 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 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 123 ILE 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 725 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1112 LEU 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 C residue 266 LEU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 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 100 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 0.0670 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098372 restraints weight = 22899.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.101336 restraints weight = 13032.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103294 restraints weight = 8985.219| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10194 Z= 0.159 Angle : 0.600 10.790 13781 Z= 0.305 Chirality : 0.043 0.173 1572 Planarity : 0.003 0.035 1742 Dihedral : 4.909 32.350 1357 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.89 % Allowed : 24.26 % 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 (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: -1.63 (0.24), residues: 1208 helix: 0.38 (0.47), residues: 137 sheet: -0.10 (0.25), residues: 417 loop : -2.15 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 562 HIS 0.009 0.001 HIS C 258 PHE 0.022 0.001 PHE C 270 TYR 0.023 0.001 TYR A 452 ARG 0.008 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3032.81 seconds wall clock time: 55 minutes 27.58 seconds (3327.58 seconds total)