Starting phenix.real_space_refine on Tue Aug 4 23:45:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1j_65549/08_2026/9w1j_65549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1j_65549/08_2026/9w1j_65549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w1j_65549/08_2026/9w1j_65549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1j_65549/08_2026/9w1j_65549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w1j_65549/08_2026/9w1j_65549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1j_65549/08_2026/9w1j_65549.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.082 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 52 5.16 5 C 4753 2.51 5 N 1266 2.21 5 O 1297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7368 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 60 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 834 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2364 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 286} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 13, 'ASN:plan1': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7368 At special positions: 0 Unit cell: (70.3625, 98.5075, 129.9, 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 52 16.00 O 1297 8.00 N 1266 7.00 C 4753 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 181 " 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: 0.47 Conformation dependent library (CDL) restraints added in 455.4 milliseconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 36.9% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.588A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.747A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.752A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.543A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.602A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.767A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.521A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.775A pdb=" N LEU R 35 " --> pdb=" O TRP R 31 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS R 61 " --> pdb=" O ILE R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 95 Processing helix chain 'R' and resid 111 through 137 Processing helix chain 'R' and resid 144 through 163 Processing helix chain 'R' and resid 191 through 227 removed outlier: 3.606A pdb=" N LEU R 195 " --> pdb=" O GLY R 191 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) Proline residue: R 209 - end of helix Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.527A pdb=" N LEU R 242 " --> pdb=" O ASN R 238 " (cutoff:3.500A) Proline residue: R 265 - end of helix removed outlier: 4.080A pdb=" N PHE R 270 " --> pdb=" O TYR R 266 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE R 271 " --> pdb=" O HIS R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 283 removed outlier: 3.736A pdb=" N HIS R 282 " --> pdb=" O ILE R 279 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS R 283 " --> pdb=" O TYR R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 298 Processing helix chain 'R' and resid 301 through 309 removed outlier: 3.817A pdb=" N ILE R 305 " --> pdb=" O MET R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 321 removed outlier: 3.538A pdb=" N GLY R 317 " --> pdb=" O ARG R 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 29 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.211A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.573A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 170 through 174 removed outlier: 3.591A pdb=" N LYS R 180 " --> pdb=" O THR R 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.656A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.844A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.796A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.561A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.601A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.685A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.764A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.68 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: 2337 1.34 - 1.46: 1958 1.46 - 1.58: 3171 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 7540 Sorted by residual: bond pdb=" CG LEU R 111 " pdb=" CD2 LEU R 111 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CB PRO A 332 " pdb=" CG PRO A 332 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.16e+00 bond pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" C GLY R 231 " pdb=" N HIS R 232 " ideal model delta sigma weight residual 1.333 1.346 -0.013 1.30e-02 5.92e+03 9.26e-01 bond pdb=" CG ARG A 283 " pdb=" CD ARG A 283 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.06e-01 ... (remaining 7535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 10135 2.07 - 4.14: 107 4.14 - 6.20: 22 6.20 - 8.27: 3 8.27 - 10.34: 2 Bond angle restraints: 10269 Sorted by residual: angle pdb=" CA LYS A 34 " pdb=" CB LYS A 34 " pdb=" CG LYS A 34 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB MET R 252 " pdb=" CG MET R 252 " pdb=" SD MET R 252 " ideal model delta sigma weight residual 112.70 122.78 -10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA LEU R 77 " pdb=" CB LEU R 77 " pdb=" CG LEU R 77 " ideal model delta sigma weight residual 116.30 126.64 -10.34 3.50e+00 8.16e-02 8.73e+00 angle pdb=" CB ARG R 313 " pdb=" CG ARG R 313 " pdb=" CD ARG R 313 " ideal model delta sigma weight residual 111.30 117.24 -5.94 2.30e+00 1.89e-01 6.66e+00 angle pdb=" N TYR R 169 " pdb=" CA TYR R 169 " pdb=" C TYR R 169 " ideal model delta sigma weight residual 114.09 110.20 3.89 1.55e+00 4.16e-01 6.29e+00 ... (remaining 10264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3781 17.66 - 35.33: 437 35.33 - 52.99: 117 52.99 - 70.65: 22 70.65 - 88.31: 9 Dihedral angle restraints: 4366 sinusoidal: 1526 harmonic: 2840 Sorted by residual: dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA HIS R 96 " pdb=" C HIS R 96 " pdb=" N ASN R 97 " pdb=" CA ASN R 97 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU R 111 " pdb=" C LEU R 111 " pdb=" N PHE R 112 " pdb=" CA PHE R 112 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 689 0.029 - 0.058: 311 0.058 - 0.087: 111 0.087 - 0.116: 60 0.116 - 0.145: 18 Chirality restraints: 1189 Sorted by residual: chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CB VAL R 255 " pdb=" CA VAL R 255 " pdb=" CG1 VAL R 255 " pdb=" CG2 VAL R 255 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1186 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 204 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C LEU R 204 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU R 204 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE R 205 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 164 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO R 165 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO R 165 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 165 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 283 " -0.126 9.50e-02 1.11e+02 5.72e-02 2.64e+00 pdb=" NE ARG A 283 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 283 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 283 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 283 " 0.000 2.00e-02 2.50e+03 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 953 2.75 - 3.29: 6792 3.29 - 3.82: 12302 3.82 - 4.36: 14308 4.36 - 4.90: 25919 Nonbonded interactions: 60274 Sorted by model distance: nonbonded pdb=" OG SER A 251 " pdb=" O LYS A 293 " model vdw 2.212 3.040 nonbonded pdb=" O VAL R 119 " pdb=" OG SER R 123 " model vdw 2.226 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.236 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.251 3.040 nonbonded pdb=" O ASN R 311 " pdb=" ND1 HIS R 312 " model vdw 2.261 3.120 ... (remaining 60269 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7542 Z= 0.156 Angle : 0.584 10.341 10273 Z= 0.300 Chirality : 0.042 0.145 1189 Planarity : 0.004 0.057 1283 Dihedral : 16.950 88.315 2522 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.43 % Allowed : 28.67 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.27), residues: 949 helix: 1.61 (0.29), residues: 322 sheet: -0.07 (0.33), residues: 206 loop : -0.88 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 283 TYR 0.015 0.001 TYR R 169 PHE 0.021 0.001 PHE R 101 TRP 0.011 0.001 TRP R 99 HIS 0.007 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 7540) covalent geometry : angle 0.58348 / 0.30 (10269) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 0.75191 / 0.39 ( 4) hydrogen bonds : bond 0.17181 / 11.82 ( 362) hydrogen bonds : angle 6.83325 / 4.91 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: R 112 PHE cc_start: 0.7804 (t80) cc_final: 0.7468 (t80) outliers start: 25 outliers final: 21 residues processed: 112 average time/residue: 0.3854 time to fit residues: 46.7476 Evaluate side-chains 113 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 69 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.162995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131439 restraints weight = 9002.282| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.60 r_work: 0.3433 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7542 Z= 0.122 Angle : 0.523 8.327 10273 Z= 0.276 Chirality : 0.041 0.130 1189 Planarity : 0.004 0.038 1283 Dihedral : 6.178 56.714 1077 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.57 % Allowed : 25.79 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.27), residues: 949 helix: 1.77 (0.29), residues: 326 sheet: 0.15 (0.35), residues: 208 loop : -0.88 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 283 TYR 0.011 0.001 TYR N 95 PHE 0.021 0.001 PHE R 101 TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7540) covalent geometry : angle 0.52325 / 0.28 (10269) SS BOND : bond 0.00118 / 0.07 ( 2) SS BOND : angle 0.70579 / 0.37 ( 4) hydrogen bonds : bond 0.04256 / 2.87 ( 362) hydrogen bonds : angle 4.94317 / 3.51 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8050 (t0) cc_final: 0.7751 (t0) REVERT: R 96 HIS cc_start: 0.7036 (t70) cc_final: 0.6666 (t70) REVERT: R 112 PHE cc_start: 0.7814 (t80) cc_final: 0.7564 (t80) REVERT: R 169 TYR cc_start: 0.6421 (m-80) cc_final: 0.6124 (m-80) REVERT: R 232 HIS cc_start: 0.4791 (OUTLIER) cc_final: 0.3760 (p90) REVERT: B 59 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8558 (m-80) outliers start: 26 outliers final: 9 residues processed: 132 average time/residue: 0.3870 time to fit residues: 55.3058 Evaluate side-chains 111 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 69 ASN R 140 GLN B 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131379 restraints weight = 8996.329| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.61 r_work: 0.3451 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7542 Z= 0.115 Angle : 0.504 9.086 10273 Z= 0.266 Chirality : 0.041 0.130 1189 Planarity : 0.004 0.039 1283 Dihedral : 5.004 54.445 1055 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.70 % Allowed : 25.79 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.27), residues: 949 helix: 1.80 (0.29), residues: 326 sheet: 0.21 (0.35), residues: 210 loop : -0.89 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 283 TYR 0.011 0.001 TYR N 95 PHE 0.015 0.001 PHE R 101 TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7540) covalent geometry : angle 0.50421 / 0.27 (10269) SS BOND : bond 0.00019 / 0.01 ( 2) SS BOND : angle 0.64560 / 0.34 ( 4) hydrogen bonds : bond 0.03969 / 2.67 ( 362) hydrogen bonds : angle 4.67409 / 3.30 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8069 (t0) cc_final: 0.7766 (t0) REVERT: R 96 HIS cc_start: 0.7166 (t70) cc_final: 0.6783 (t70) REVERT: R 140 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7539 (tp-100) REVERT: R 169 TYR cc_start: 0.6525 (m-80) cc_final: 0.6250 (m-80) REVERT: R 232 HIS cc_start: 0.4761 (OUTLIER) cc_final: 0.2878 (p90) REVERT: R 241 HIS cc_start: 0.5680 (OUTLIER) cc_final: 0.5427 (t-170) REVERT: R 283 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7043 (tttp) REVERT: B 59 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: B 243 THR cc_start: 0.8853 (p) cc_final: 0.8652 (p) outliers start: 27 outliers final: 12 residues processed: 129 average time/residue: 0.4085 time to fit residues: 56.6765 Evaluate side-chains 122 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 CYS Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 HIS Chi-restraints excluded: chain R residue 283 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 304 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.0170 chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 69 ASN R 282 HIS B 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.163859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131696 restraints weight = 9158.394| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.71 r_work: 0.3446 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7542 Z= 0.106 Angle : 0.494 9.429 10273 Z= 0.259 Chirality : 0.040 0.130 1189 Planarity : 0.003 0.038 1283 Dihedral : 4.672 53.186 1052 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.80 % Allowed : 25.65 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 949 helix: 1.87 (0.29), residues: 326 sheet: 0.26 (0.34), residues: 220 loop : -0.90 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.011 0.001 TYR N 95 PHE 0.014 0.001 PHE R 101 TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 7540) covalent geometry : angle 0.49386 / 0.26 (10269) SS BOND : bond 0.00047 / 0.03 ( 2) SS BOND : angle 0.65106 / 0.34 ( 4) hydrogen bonds : bond 0.03751 / 2.51 ( 362) hydrogen bonds : angle 4.52658 / 3.20 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7982 (t0) cc_final: 0.7664 (t0) REVERT: R 64 MET cc_start: 0.6394 (ptp) cc_final: 0.5947 (ptp) REVERT: R 96 HIS cc_start: 0.7313 (t70) cc_final: 0.6913 (t70) REVERT: R 140 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7640 (tp-100) REVERT: R 169 TYR cc_start: 0.6614 (m-80) cc_final: 0.6317 (m-80) REVERT: R 232 HIS cc_start: 0.4592 (OUTLIER) cc_final: 0.2538 (p90) REVERT: R 283 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7046 (tttp) REVERT: B 59 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8590 (m-80) REVERT: B 243 THR cc_start: 0.8861 (p) cc_final: 0.8656 (p) outliers start: 35 outliers final: 18 residues processed: 133 average time/residue: 0.3780 time to fit residues: 54.3290 Evaluate side-chains 121 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 283 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 304 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 140 GLN ** R 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 HIS R 311 ASN B 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128950 restraints weight = 9012.408| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.68 r_work: 0.3395 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7542 Z= 0.138 Angle : 0.523 9.824 10273 Z= 0.273 Chirality : 0.041 0.134 1189 Planarity : 0.004 0.039 1283 Dihedral : 4.790 51.653 1052 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.94 % Allowed : 26.06 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.27), residues: 949 helix: 1.80 (0.28), residues: 330 sheet: 0.04 (0.33), residues: 225 loop : -0.96 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.013 0.001 TYR N 95 PHE 0.012 0.001 PHE R 101 TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7540) covalent geometry : angle 0.52278 / 0.27 (10269) SS BOND : bond 0.00096 / 0.06 ( 2) SS BOND : angle 0.73253 / 0.39 ( 4) hydrogen bonds : bond 0.04059 / 2.73 ( 362) hydrogen bonds : angle 4.57723 / 3.24 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7942 (t0) cc_final: 0.7613 (t0) REVERT: R 64 MET cc_start: 0.6343 (ptp) cc_final: 0.5871 (ptp) REVERT: R 140 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7646 (tp-100) REVERT: R 169 TYR cc_start: 0.6830 (m-80) cc_final: 0.6554 (m-80) REVERT: R 232 HIS cc_start: 0.4588 (OUTLIER) cc_final: 0.2429 (p90) REVERT: R 283 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7064 (tttp) REVERT: B 59 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: B 243 THR cc_start: 0.8890 (p) cc_final: 0.8668 (p) outliers start: 36 outliers final: 20 residues processed: 129 average time/residue: 0.3393 time to fit residues: 47.2969 Evaluate side-chains 125 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 283 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 304 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 69 ASN R 282 HIS B 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126463 restraints weight = 9112.229| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.69 r_work: 0.3383 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7542 Z= 0.213 Angle : 0.596 9.431 10273 Z= 0.312 Chirality : 0.044 0.143 1189 Planarity : 0.004 0.041 1283 Dihedral : 5.092 48.021 1052 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.21 % Allowed : 26.47 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.27), residues: 949 helix: 1.57 (0.28), residues: 327 sheet: -0.07 (0.33), residues: 225 loop : -1.02 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.016 0.002 TYR N 95 PHE 0.012 0.002 PHE A 212 TRP 0.020 0.002 TRP B 82 HIS 0.008 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 ( 7540) covalent geometry : angle 0.59620 / 0.31 (10269) SS BOND : bond 0.00189 / 0.12 ( 2) SS BOND : angle 0.86096 / 0.43 ( 4) hydrogen bonds : bond 0.04649 / 3.12 ( 362) hydrogen bonds : angle 4.77639 / 3.39 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8126 (t0) cc_final: 0.7790 (t0) REVERT: R 61 HIS cc_start: 0.5723 (m90) cc_final: 0.5501 (m90) REVERT: R 166 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6992 (mt0) REVERT: R 169 TYR cc_start: 0.6973 (m-80) cc_final: 0.6690 (m-80) REVERT: R 232 HIS cc_start: 0.4495 (OUTLIER) cc_final: 0.2407 (p90) REVERT: R 283 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7119 (tttp) REVERT: B 59 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8702 (m-80) outliers start: 38 outliers final: 19 residues processed: 129 average time/residue: 0.4026 time to fit residues: 56.1067 Evaluate side-chains 120 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 181 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 283 LYS Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 304 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 166 GLN ** R 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.162089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.129868 restraints weight = 9100.125| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.71 r_work: 0.3404 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7542 Z= 0.115 Angle : 0.521 8.798 10273 Z= 0.273 Chirality : 0.041 0.132 1189 Planarity : 0.004 0.039 1283 Dihedral : 4.729 48.051 1052 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.39 % Allowed : 27.30 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 949 helix: 1.76 (0.29), residues: 327 sheet: 0.26 (0.34), residues: 208 loop : -1.01 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 313 TYR 0.010 0.001 TYR A 339 PHE 0.008 0.001 PHE A 212 TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7540) covalent geometry : angle 0.52115 / 0.27 (10269) SS BOND : bond 0.00052 / 0.03 ( 2) SS BOND : angle 0.71388 / 0.37 ( 4) hydrogen bonds : bond 0.03868 / 2.61 ( 362) hydrogen bonds : angle 4.50712 / 3.19 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7987 (t0) cc_final: 0.7667 (t0) REVERT: R 140 GLN cc_start: 0.7787 (tp40) cc_final: 0.7492 (tp-100) REVERT: R 169 TYR cc_start: 0.6866 (m-80) cc_final: 0.6540 (m-80) REVERT: R 283 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7068 (tttp) REVERT: R 313 ARG cc_start: 0.7627 (tpp-160) cc_final: 0.7310 (tpp80) REVERT: B 59 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: B 243 THR cc_start: 0.8910 (p) cc_final: 0.8693 (p) REVERT: B 256 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7941 (mtm180) outliers start: 32 outliers final: 14 residues processed: 126 average time/residue: 0.4159 time to fit residues: 56.3322 Evaluate side-chains 113 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 CYS Chi-restraints excluded: chain R residue 283 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 256 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 282 HIS B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127063 restraints weight = 9156.987| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.70 r_work: 0.3385 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7542 Z= 0.186 Angle : 0.587 10.545 10273 Z= 0.303 Chirality : 0.043 0.140 1189 Planarity : 0.004 0.041 1283 Dihedral : 4.704 47.090 1050 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.84 % Allowed : 28.40 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 949 helix: 1.58 (0.28), residues: 327 sheet: 0.08 (0.34), residues: 213 loop : -1.05 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.014 0.001 TYR N 95 PHE 0.011 0.001 PHE A 212 TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 7540) covalent geometry : angle 0.58694 / 0.30 (10269) SS BOND : bond 0.00284 / 0.18 ( 2) SS BOND : angle 0.69903 / 0.36 ( 4) hydrogen bonds : bond 0.04444 / 3.00 ( 362) hydrogen bonds : angle 4.70589 / 3.34 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8124 (t0) cc_final: 0.7789 (t0) REVERT: L 10 MET cc_start: 0.8733 (mtp) cc_final: 0.8052 (mtp) REVERT: R 140 GLN cc_start: 0.7826 (tp40) cc_final: 0.7534 (tp-100) REVERT: R 232 HIS cc_start: 0.4702 (OUTLIER) cc_final: 0.2701 (p-80) REVERT: R 283 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7103 (tttp) REVERT: B 59 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8606 (m-80) outliers start: 28 outliers final: 18 residues processed: 119 average time/residue: 0.3509 time to fit residues: 45.1645 Evaluate side-chains 115 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 283 LYS Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 HIS B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128700 restraints weight = 9092.989| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.70 r_work: 0.3397 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7542 Z= 0.137 Angle : 0.552 10.355 10273 Z= 0.285 Chirality : 0.041 0.135 1189 Planarity : 0.004 0.040 1283 Dihedral : 4.321 41.858 1048 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.43 % Allowed : 28.81 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 949 helix: 1.66 (0.28), residues: 332 sheet: 0.21 (0.35), residues: 206 loop : -1.09 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 313 TYR 0.014 0.001 TYR N 60 PHE 0.009 0.001 PHE A 212 TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7540) covalent geometry : angle 0.55230 / 0.28 (10269) SS BOND : bond 0.00129 / 0.08 ( 2) SS BOND : angle 0.63441 / 0.32 ( 4) hydrogen bonds : bond 0.04078 / 2.76 ( 362) hydrogen bonds : angle 4.56276 / 3.23 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8135 (t0) cc_final: 0.7792 (t0) REVERT: L 10 MET cc_start: 0.8708 (mtp) cc_final: 0.8404 (mtp) REVERT: R 140 GLN cc_start: 0.7824 (tp40) cc_final: 0.7530 (tp-100) REVERT: R 232 HIS cc_start: 0.4637 (OUTLIER) cc_final: 0.2825 (p-80) REVERT: R 283 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7135 (tttp) REVERT: R 312 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6878 (p-80) REVERT: R 313 ARG cc_start: 0.7746 (tpp-160) cc_final: 0.7319 (tpp80) REVERT: B 59 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8545 (m-80) REVERT: B 256 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7933 (mtm180) outliers start: 25 outliers final: 16 residues processed: 114 average time/residue: 0.3708 time to fit residues: 45.7495 Evaluate side-chains 115 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 283 LYS Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 256 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 HIS B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.160845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128669 restraints weight = 9091.842| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.70 r_work: 0.3389 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7542 Z= 0.136 Angle : 0.554 10.272 10273 Z= 0.284 Chirality : 0.041 0.134 1189 Planarity : 0.004 0.040 1283 Dihedral : 4.273 41.407 1048 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.84 % Allowed : 28.67 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 949 helix: 1.72 (0.28), residues: 332 sheet: 0.21 (0.35), residues: 209 loop : -1.12 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 313 TYR 0.015 0.001 TYR N 60 PHE 0.009 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 7540) covalent geometry : angle 0.55361 / 0.28 (10269) SS BOND : bond 0.00110 / 0.07 ( 2) SS BOND : angle 0.69053 / 0.36 ( 4) hydrogen bonds : bond 0.04026 / 2.71 ( 362) hydrogen bonds : angle 4.52964 / 3.20 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8124 (t0) cc_final: 0.7782 (t0) REVERT: L 10 MET cc_start: 0.8704 (mtp) cc_final: 0.8401 (mtp) REVERT: R 140 GLN cc_start: 0.7820 (tp40) cc_final: 0.7520 (tp-100) REVERT: R 232 HIS cc_start: 0.4647 (OUTLIER) cc_final: 0.2840 (p-80) REVERT: R 283 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7119 (tttp) REVERT: B 59 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8576 (m-80) REVERT: B 256 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7955 (mtm180) outliers start: 28 outliers final: 18 residues processed: 118 average time/residue: 0.4329 time to fit residues: 54.9257 Evaluate side-chains 117 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 283 LYS Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 256 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 0.0040 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 HIS B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129639 restraints weight = 9032.667| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.70 r_work: 0.3399 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7542 Z= 0.121 Angle : 0.547 10.195 10273 Z= 0.281 Chirality : 0.041 0.132 1189 Planarity : 0.004 0.040 1283 Dihedral : 4.183 40.687 1048 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.02 % Allowed : 29.77 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 949 helix: 1.79 (0.29), residues: 332 sheet: 0.31 (0.35), residues: 204 loop : -1.11 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 313 TYR 0.015 0.001 TYR N 60 PHE 0.009 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7540) covalent geometry : angle 0.54672 / 0.28 (10269) SS BOND : bond 0.00089 / 0.06 ( 2) SS BOND : angle 0.66750 / 0.35 ( 4) hydrogen bonds : bond 0.03848 / 2.60 ( 362) hydrogen bonds : angle 4.45658 / 3.15 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.14 seconds wall clock time: 40 minutes 3.89 seconds (2403.89 seconds total)