Starting phenix.real_space_refine on Fri Aug 22 22:26:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9x_27967/08_2025/8e9x_27967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9x_27967/08_2025/8e9x_27967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e9x_27967/08_2025/8e9x_27967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9x_27967/08_2025/8e9x_27967.map" model { file = "/net/cci-nas-00/data/ceres_data/8e9x_27967/08_2025/8e9x_27967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9x_27967/08_2025/8e9x_27967.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5364 2.51 5 N 1401 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8380 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2124 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1666 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2485 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'WEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.62, per 1000 atoms: 0.19 Number of scatterers: 8380 At special positions: 0 Unit cell: (91.52, 117.04, 128.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1554 8.00 N 1401 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 429 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 350.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 28 through 60 removed outlier: 3.652A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.611A pdb=" N PHE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 removed outlier: 3.880A pdb=" N THR A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 136 removed outlier: 4.162A pdb=" N ASN A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 170 removed outlier: 3.616A pdb=" N TRP A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.854A pdb=" N LEU A 190 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 191 " --> pdb=" O GLN A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 191' Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 204 through 221 removed outlier: 3.561A pdb=" N MET A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 4.038A pdb=" N LYS A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.749A pdb=" N LEU A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.530A pdb=" N SER A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.587A pdb=" N ARG A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 removed outlier: 3.994A pdb=" N LYS B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.906A pdb=" N ILE B 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.474A pdb=" N ILE B 94 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS B 95 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 127 removed outlier: 4.168A pdb=" N HIS B 116 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 153 removed outlier: 3.600A pdb=" N GLU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 182 removed outlier: 3.670A pdb=" N ALA B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 222 removed outlier: 4.058A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.558A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.551A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.628A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.533A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.842A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 52 removed outlier: 3.786A pdb=" N LYS B 51 " --> pdb=" O HIS B 70 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 31 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE B 81 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 33 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS B 32 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE B 104 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 34 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS B 106 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 36 " --> pdb=" O CYS B 106 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASP B 108 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE B 105 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN B 141 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 107 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.600A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.714A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.373A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.211A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.820A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.586A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.743A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.540A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.505A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.505A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.406A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1176 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: 0.88 Time building geometry restraints manager: 0.85 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: 2673 1.34 - 1.46: 2103 1.46 - 1.58: 3703 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 8565 Sorted by residual: bond pdb=" C01 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.455 1.286 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C06 WEC A 501 " pdb=" N07 WEC A 501 " ideal model delta sigma weight residual 1.292 1.452 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C06 WEC A 501 " pdb=" N05 WEC A 501 " ideal model delta sigma weight residual 1.373 1.498 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C03 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.461 1.371 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C22 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.459 1.372 0.087 2.00e-02 2.50e+03 1.88e+01 ... (remaining 8560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11436 1.71 - 3.41: 193 3.41 - 5.12: 30 5.12 - 6.82: 7 6.82 - 8.53: 4 Bond angle restraints: 11670 Sorted by residual: angle pdb=" N TRP A 440 " pdb=" CA TRP A 440 " pdb=" C TRP A 440 " ideal model delta sigma weight residual 111.33 117.20 -5.87 1.21e+00 6.83e-01 2.35e+01 angle pdb=" C TYR A 439 " pdb=" CA TYR A 439 " pdb=" CB TYR A 439 " ideal model delta sigma weight residual 110.56 102.09 8.47 1.83e+00 2.99e-01 2.14e+01 angle pdb=" N ASN B 202 " pdb=" CA ASN B 202 " pdb=" C ASN B 202 " ideal model delta sigma weight residual 114.12 108.45 5.67 1.39e+00 5.18e-01 1.66e+01 angle pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" O ARG E 179 " ideal model delta sigma weight residual 120.98 116.91 4.07 1.24e+00 6.50e-01 1.08e+01 angle pdb=" C ARG A 178 " pdb=" CA ARG A 178 " pdb=" CB ARG A 178 " ideal model delta sigma weight residual 111.78 104.97 6.81 2.20e+00 2.07e-01 9.57e+00 ... (remaining 11665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 4503 15.12 - 30.24: 400 30.24 - 45.37: 82 45.37 - 60.49: 19 60.49 - 75.61: 6 Dihedral angle restraints: 5010 sinusoidal: 1791 harmonic: 3219 Sorted by residual: dihedral pdb=" CA THR E 160 " pdb=" C THR E 160 " pdb=" N TYR E 161 " pdb=" CA TYR E 161 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA CYS A 426 " pdb=" C CYS A 426 " pdb=" N GLN A 427 " pdb=" CA GLN A 427 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB CYS A 105 " pdb=" SG CYS A 105 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -117.07 31.07 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 5007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1135 0.054 - 0.108: 189 0.108 - 0.161: 31 0.161 - 0.215: 6 0.215 - 0.269: 1 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA LEU A 52 " pdb=" N LEU A 52 " pdb=" C LEU A 52 " pdb=" CB LEU A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TRP A 440 " pdb=" N TRP A 440 " pdb=" C TRP A 440 " pdb=" CB TRP A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN A 50 " pdb=" N ASN A 50 " pdb=" C ASN A 50 " pdb=" CB ASN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1359 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 179 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C ARG E 179 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG E 179 " 0.021 2.00e-02 2.50e+03 pdb=" N MET E 180 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 202 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C ASN B 202 " 0.024 2.00e-02 2.50e+03 pdb=" O ASN B 202 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA B 203 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 153 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 154 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " 0.019 5.00e-02 4.00e+02 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 567 2.74 - 3.28: 8267 3.28 - 3.82: 13795 3.82 - 4.36: 16888 4.36 - 4.90: 29210 Nonbonded interactions: 68727 Sorted by model distance: nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 88 " pdb=" OD2 ASP C 186 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.271 3.040 nonbonded pdb=" ND2 ASN C 340 " pdb=" OD1 ASN D 59 " model vdw 2.319 3.120 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.328 3.040 ... (remaining 68722 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 individual isotropic 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.005 0.169 8568 Z= 0.256 Angle : 0.554 8.530 11676 Z= 0.312 Chirality : 0.044 0.269 1362 Planarity : 0.003 0.034 1470 Dihedral : 12.406 75.609 2925 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1093 helix: 0.51 (0.28), residues: 359 sheet: 0.59 (0.31), residues: 286 loop : -1.00 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 179 TYR 0.023 0.001 TYR E 178 PHE 0.012 0.001 PHE A 189 TRP 0.021 0.001 TRP C 339 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8565) covalent geometry : angle 0.55331 (11670) SS BOND : bond 0.00469 ( 3) SS BOND : angle 1.12329 ( 6) hydrogen bonds : bond 0.24186 ( 409) hydrogen bonds : angle 7.79674 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.200 Fit side-chains REVERT: A 410 ILE cc_start: 0.7951 (mm) cc_final: 0.7667 (mm) REVERT: B 29 LYS cc_start: 0.7759 (mppt) cc_final: 0.7504 (mppt) REVERT: B 81 PHE cc_start: 0.8308 (m-80) cc_final: 0.7896 (m-80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.3395 time to fit residues: 70.1500 Evaluate side-chains 168 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.0020 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 128 ASN B 202 ASN B 217 ASN C 88 ASN C 110 ASN C 259 GLN C 293 ASN E 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110463 restraints weight = 11950.710| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.74 r_work: 0.3349 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8568 Z= 0.156 Angle : 0.551 7.565 11676 Z= 0.290 Chirality : 0.042 0.165 1362 Planarity : 0.004 0.038 1470 Dihedral : 4.359 28.701 1200 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.84 % Allowed : 10.33 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.26), residues: 1093 helix: 1.41 (0.28), residues: 355 sheet: 0.76 (0.31), residues: 282 loop : -0.78 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.016 0.001 TYR A 92 PHE 0.013 0.002 PHE C 151 TRP 0.019 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8565) covalent geometry : angle 0.55023 (11670) SS BOND : bond 0.00601 ( 3) SS BOND : angle 1.14335 ( 6) hydrogen bonds : bond 0.04712 ( 409) hydrogen bonds : angle 4.74854 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.286 Fit side-chains REVERT: A 136 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8131 (mtmm) REVERT: A 439 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: B 29 LYS cc_start: 0.8175 (mppt) cc_final: 0.7844 (mppt) REVERT: B 217 ASN cc_start: 0.7956 (m-40) cc_final: 0.7746 (m110) REVERT: C 153 ASP cc_start: 0.7740 (p0) cc_final: 0.7531 (p0) outliers start: 16 outliers final: 5 residues processed: 187 average time/residue: 0.3697 time to fit residues: 75.3789 Evaluate side-chains 176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 202 ASN B 218 ASN C 88 ASN C 110 ASN C 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109072 restraints weight = 11843.677| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.76 r_work: 0.3329 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8568 Z= 0.173 Angle : 0.545 7.662 11676 Z= 0.284 Chirality : 0.042 0.153 1362 Planarity : 0.004 0.039 1470 Dihedral : 4.388 26.517 1200 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.56 % Allowed : 11.94 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1093 helix: 1.66 (0.28), residues: 354 sheet: 0.67 (0.31), residues: 282 loop : -0.88 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.017 0.002 TYR A 92 PHE 0.015 0.002 PHE A 189 TRP 0.017 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8565) covalent geometry : angle 0.54506 (11670) SS BOND : bond 0.00591 ( 3) SS BOND : angle 1.09314 ( 6) hydrogen bonds : bond 0.04527 ( 409) hydrogen bonds : angle 4.53379 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 73 SER cc_start: 0.8052 (p) cc_final: 0.7841 (t) REVERT: A 439 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: B 29 LYS cc_start: 0.8229 (mppt) cc_final: 0.7922 (mppt) REVERT: B 217 ASN cc_start: 0.7980 (m-40) cc_final: 0.7768 (m110) REVERT: C 153 ASP cc_start: 0.7779 (p0) cc_final: 0.7561 (p0) outliers start: 31 outliers final: 18 residues processed: 184 average time/residue: 0.3416 time to fit residues: 68.7557 Evaluate side-chains 187 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 128 ASN B 202 ASN C 88 ASN C 110 ASN C 293 ASN E 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109930 restraints weight = 11907.815| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.75 r_work: 0.3340 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8568 Z= 0.148 Angle : 0.517 7.450 11676 Z= 0.270 Chirality : 0.041 0.141 1362 Planarity : 0.004 0.040 1470 Dihedral : 4.316 25.134 1200 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.67 % Allowed : 13.55 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.26), residues: 1093 helix: 1.84 (0.29), residues: 350 sheet: 0.64 (0.30), residues: 282 loop : -0.85 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 219 TYR 0.014 0.001 TYR A 92 PHE 0.014 0.001 PHE A 189 TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8565) covalent geometry : angle 0.51699 (11670) SS BOND : bond 0.00525 ( 3) SS BOND : angle 1.03891 ( 6) hydrogen bonds : bond 0.04017 ( 409) hydrogen bonds : angle 4.34137 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.5967 (ppp) cc_final: 0.5653 (ppp) REVERT: A 208 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7868 (t) REVERT: A 439 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: B 217 ASN cc_start: 0.7930 (m-40) cc_final: 0.7714 (m110) REVERT: C 153 ASP cc_start: 0.7780 (p0) cc_final: 0.7572 (p0) outliers start: 32 outliers final: 16 residues processed: 180 average time/residue: 0.4168 time to fit residues: 81.8771 Evaluate side-chains 180 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN B 70 HIS B 141 ASN B 202 ASN C 293 ASN E 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109145 restraints weight = 11910.861| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.76 r_work: 0.3329 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8568 Z= 0.175 Angle : 0.538 7.549 11676 Z= 0.281 Chirality : 0.043 0.165 1362 Planarity : 0.004 0.036 1470 Dihedral : 4.414 24.924 1200 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.33 % Allowed : 14.24 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.26), residues: 1093 helix: 1.84 (0.28), residues: 349 sheet: 0.63 (0.30), residues: 282 loop : -0.89 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 219 TYR 0.016 0.001 TYR A 92 PHE 0.015 0.002 PHE A 189 TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8565) covalent geometry : angle 0.53760 (11670) SS BOND : bond 0.00569 ( 3) SS BOND : angle 1.08861 ( 6) hydrogen bonds : bond 0.04130 ( 409) hydrogen bonds : angle 4.36661 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.6024 (ppp) cc_final: 0.5671 (ppp) REVERT: A 208 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7866 (t) REVERT: A 439 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: B 217 ASN cc_start: 0.7967 (m-40) cc_final: 0.7755 (m110) REVERT: C 153 ASP cc_start: 0.7772 (p0) cc_final: 0.7559 (p0) outliers start: 29 outliers final: 21 residues processed: 181 average time/residue: 0.3744 time to fit residues: 74.0266 Evaluate side-chains 190 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN B 202 ASN B 218 ASN C 239 ASN C 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107997 restraints weight = 11765.710| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.74 r_work: 0.3311 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8568 Z= 0.227 Angle : 0.576 7.950 11676 Z= 0.300 Chirality : 0.044 0.158 1362 Planarity : 0.004 0.038 1470 Dihedral : 4.654 34.154 1200 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.79 % Allowed : 15.04 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.26), residues: 1093 helix: 1.75 (0.28), residues: 350 sheet: 0.53 (0.30), residues: 281 loop : -0.90 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 219 TYR 0.019 0.002 TYR A 92 PHE 0.017 0.002 PHE C 151 TRP 0.015 0.002 TRP C 169 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 8565) covalent geometry : angle 0.57507 (11670) SS BOND : bond 0.00659 ( 3) SS BOND : angle 1.19743 ( 6) hydrogen bonds : bond 0.04456 ( 409) hydrogen bonds : angle 4.44845 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.6011 (ppp) cc_final: 0.5671 (ppp) REVERT: A 208 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7901 (t) REVERT: A 439 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: B 217 ASN cc_start: 0.7980 (m-40) cc_final: 0.7762 (m110) REVERT: C 153 ASP cc_start: 0.7770 (p0) cc_final: 0.7554 (p0) outliers start: 33 outliers final: 25 residues processed: 183 average time/residue: 0.3749 time to fit residues: 75.3004 Evaluate side-chains 202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN B 202 ASN C 293 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108384 restraints weight = 11900.034| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.76 r_work: 0.3316 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8568 Z= 0.189 Angle : 0.555 7.568 11676 Z= 0.290 Chirality : 0.043 0.160 1362 Planarity : 0.004 0.037 1470 Dihedral : 4.600 34.846 1200 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.79 % Allowed : 15.84 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.26), residues: 1093 helix: 1.81 (0.28), residues: 349 sheet: 0.49 (0.30), residues: 281 loop : -0.92 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 219 TYR 0.015 0.002 TYR A 92 PHE 0.015 0.002 PHE A 189 TRP 0.016 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 8565) covalent geometry : angle 0.55405 (11670) SS BOND : bond 0.00618 ( 3) SS BOND : angle 1.15246 ( 6) hydrogen bonds : bond 0.04196 ( 409) hydrogen bonds : angle 4.40134 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.366 Fit side-chains REVERT: A 32 MET cc_start: 0.6035 (ppp) cc_final: 0.5698 (ppp) REVERT: A 65 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7726 (p) REVERT: A 208 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7867 (t) REVERT: A 439 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: B 217 ASN cc_start: 0.7962 (m-40) cc_final: 0.7739 (m110) REVERT: C 153 ASP cc_start: 0.7774 (p0) cc_final: 0.7562 (p0) outliers start: 33 outliers final: 27 residues processed: 187 average time/residue: 0.3847 time to fit residues: 78.9450 Evaluate side-chains 203 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 0.0000 chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN B 202 ASN C 340 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110443 restraints weight = 11891.376| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.74 r_work: 0.3348 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8568 Z= 0.115 Angle : 0.504 7.368 11676 Z= 0.265 Chirality : 0.041 0.173 1362 Planarity : 0.004 0.039 1470 Dihedral : 4.319 30.137 1200 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.21 % Allowed : 16.99 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1093 helix: 2.03 (0.29), residues: 350 sheet: 0.49 (0.31), residues: 271 loop : -0.82 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 219 TYR 0.014 0.001 TYR E 178 PHE 0.012 0.001 PHE A 189 TRP 0.019 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8565) covalent geometry : angle 0.50330 (11670) SS BOND : bond 0.00478 ( 3) SS BOND : angle 1.00217 ( 6) hydrogen bonds : bond 0.03558 ( 409) hydrogen bonds : angle 4.22965 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.291 Fit side-chains REVERT: A 32 MET cc_start: 0.5981 (ppp) cc_final: 0.5602 (ppp) REVERT: A 208 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7852 (t) REVERT: A 439 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: B 217 ASN cc_start: 0.7931 (m-40) cc_final: 0.7708 (m110) REVERT: C 153 ASP cc_start: 0.7810 (p0) cc_final: 0.7562 (p0) outliers start: 28 outliers final: 18 residues processed: 180 average time/residue: 0.3878 time to fit residues: 76.4012 Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.0030 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN B 202 ASN C 293 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110011 restraints weight = 11916.819| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.75 r_work: 0.3341 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8568 Z= 0.130 Angle : 0.513 7.435 11676 Z= 0.268 Chirality : 0.041 0.163 1362 Planarity : 0.004 0.037 1470 Dihedral : 4.310 28.865 1200 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.76 % Allowed : 17.57 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1093 helix: 2.07 (0.28), residues: 350 sheet: 0.47 (0.31), residues: 271 loop : -0.81 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 219 TYR 0.013 0.001 TYR E 178 PHE 0.012 0.001 PHE A 189 TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8565) covalent geometry : angle 0.51291 (11670) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.05689 ( 6) hydrogen bonds : bond 0.03635 ( 409) hydrogen bonds : angle 4.21765 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.329 Fit side-chains REVERT: A 32 MET cc_start: 0.6009 (ppp) cc_final: 0.5639 (ppp) REVERT: A 208 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 439 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: C 153 ASP cc_start: 0.7794 (p0) cc_final: 0.7557 (p0) REVERT: C 155 ASN cc_start: 0.8048 (t0) cc_final: 0.7842 (t0) outliers start: 24 outliers final: 17 residues processed: 177 average time/residue: 0.3961 time to fit residues: 76.7793 Evaluate side-chains 186 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 84 optimal weight: 0.0270 chunk 85 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN B 202 ASN C 293 ASN C 340 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109530 restraints weight = 11851.283| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.75 r_work: 0.3335 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8568 Z= 0.157 Angle : 0.535 7.498 11676 Z= 0.279 Chirality : 0.042 0.161 1362 Planarity : 0.004 0.039 1470 Dihedral : 4.374 25.439 1200 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.64 % Allowed : 17.80 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.26), residues: 1093 helix: 2.02 (0.28), residues: 350 sheet: 0.49 (0.31), residues: 271 loop : -0.83 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.013 0.001 TYR E 178 PHE 0.014 0.002 PHE C 151 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8565) covalent geometry : angle 0.53474 (11670) SS BOND : bond 0.00556 ( 3) SS BOND : angle 1.10380 ( 6) hydrogen bonds : bond 0.03803 ( 409) hydrogen bonds : angle 4.27018 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.281 Fit side-chains REVERT: A 32 MET cc_start: 0.6006 (ppp) cc_final: 0.5678 (ppp) REVERT: A 208 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7871 (t) REVERT: A 439 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: C 153 ASP cc_start: 0.7791 (p0) cc_final: 0.7575 (p0) outliers start: 23 outliers final: 19 residues processed: 175 average time/residue: 0.3993 time to fit residues: 76.4048 Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN B 202 ASN C 293 ASN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109648 restraints weight = 11939.482| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.75 r_work: 0.3336 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8568 Z= 0.143 Angle : 0.531 7.936 11676 Z= 0.276 Chirality : 0.042 0.154 1362 Planarity : 0.004 0.037 1470 Dihedral : 4.331 22.822 1200 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.87 % Allowed : 17.34 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1093 helix: 2.04 (0.28), residues: 350 sheet: 0.50 (0.31), residues: 271 loop : -0.83 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 219 TYR 0.013 0.001 TYR E 178 PHE 0.013 0.001 PHE A 189 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8565) covalent geometry : angle 0.53034 (11670) SS BOND : bond 0.00534 ( 3) SS BOND : angle 1.06018 ( 6) hydrogen bonds : bond 0.03713 ( 409) hydrogen bonds : angle 4.25323 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.48 seconds wall clock time: 54 minutes 54.04 seconds (3294.04 seconds total)