Starting phenix.real_space_refine on Wed Feb 4 05:49:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jky_61574/02_2026/9jky_61574_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jky_61574/02_2026/9jky_61574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jky_61574/02_2026/9jky_61574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jky_61574/02_2026/9jky_61574.map" model { file = "/net/cci-nas-00/data/ceres_data/9jky_61574/02_2026/9jky_61574_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jky_61574/02_2026/9jky_61574_neut.cif" } resolution = 2.72 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= 0.020 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 67 5.16 5 C 5654 2.51 5 N 1515 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2338 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2581 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1728 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 426 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1783 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.19 Number of scatterers: 8872 At special positions: 0 Unit cell: (87.98, 118.69, 130.31, 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 67 16.00 O 1636 8.00 N 1515 7.00 C 5654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.70 Conformation dependent library (CDL) restraints added in 233.5 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 23 through 56 removed outlier: 4.297A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.722A pdb=" N LEU A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 88 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.900A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 164 removed outlier: 5.238A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.595A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 262 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 295 removed outlier: 3.779A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.512A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 32 removed outlier: 3.670A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.197A pdb=" N GLN C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.095A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.896A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.596A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.512A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.562A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.234A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.633A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.536A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.995A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.875A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.643A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.524A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.796A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 191 removed outlier: 3.700A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.662A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.662A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 5.568A pdb=" N GLU S 153 " --> pdb=" O ARG S 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.908A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.908A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1275 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: 1.57 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1437 1.31 - 1.44: 2553 1.44 - 1.56: 4981 1.56 - 1.69: 1 1.69 - 1.82: 97 Bond restraints: 9069 Sorted by residual: bond pdb=" C4 P9X A 401 " pdb=" O1 P9X A 401 " ideal model delta sigma weight residual 1.342 1.528 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" C1 P9X A 401 " pdb=" C2 P9X A 401 " ideal model delta sigma weight residual 1.550 1.385 0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" C3 P9X A 401 " pdb=" C4 P9X A 401 " ideal model delta sigma weight residual 1.357 1.506 -0.149 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C1 P9X A 401 " pdb=" O1 P9X A 401 " ideal model delta sigma weight residual 1.455 1.565 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C2 P9X A 401 " pdb=" C3 P9X A 401 " ideal model delta sigma weight residual 1.436 1.367 0.069 2.00e-02 2.50e+03 1.21e+01 ... (remaining 9064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 12114 2.11 - 4.22: 143 4.22 - 6.33: 17 6.33 - 8.45: 5 8.45 - 10.56: 3 Bond angle restraints: 12282 Sorted by residual: angle pdb=" C SER C 281 " pdb=" N PRO C 282 " pdb=" CA PRO C 282 " ideal model delta sigma weight residual 120.25 125.12 -4.87 1.35e+00 5.49e-01 1.30e+01 angle pdb=" C1 P9X A 401 " pdb=" C2 P9X A 401 " pdb=" C3 P9X A 401 " ideal model delta sigma weight residual 105.43 115.99 -10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CA TRP A 91 " pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " ideal model delta sigma weight residual 113.60 107.30 6.30 1.90e+00 2.77e-01 1.10e+01 angle pdb=" C ALA S 221 " pdb=" N GLU S 222 " pdb=" CA GLU S 222 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C ILE A 98 " pdb=" N PRO A 99 " pdb=" CA PRO A 99 " ideal model delta sigma weight residual 119.24 115.90 3.34 1.04e+00 9.25e-01 1.03e+01 ... (remaining 12277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4710 17.94 - 35.88: 507 35.88 - 53.82: 128 53.82 - 71.76: 28 71.76 - 89.70: 8 Dihedral angle restraints: 5381 sinusoidal: 2090 harmonic: 3291 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual 93.00 134.98 -41.98 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CA LYS A 15 " pdb=" C LYS A 15 " pdb=" N LYS A 16 " pdb=" CA LYS A 16 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 932 0.033 - 0.066: 293 0.066 - 0.099: 96 0.099 - 0.132: 52 0.132 - 0.165: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C1 P9X A 401 " pdb=" C2 P9X A 401 " pdb=" C6 P9X A 401 " pdb=" O1 P9X A 401 " both_signs ideal model delta sigma weight residual False 2.77 2.61 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" C PRO S 75 " pdb=" CB PRO S 75 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA PRO A 291 " pdb=" N PRO A 291 " pdb=" C PRO A 291 " pdb=" CB PRO A 291 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1371 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 290 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO A 291 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 95 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C PHE A 95 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE A 95 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 96 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO S 75 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.024 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 283 2.71 - 3.26: 8767 3.26 - 3.80: 14823 3.80 - 4.35: 18842 4.35 - 4.90: 32331 Nonbonded interactions: 75046 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.159 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.177 3.040 nonbonded pdb=" O ILE A 278 " pdb=" OG SER A 281 " model vdw 2.209 3.040 nonbonded pdb=" O LEU A 257 " pdb=" OG SER A 261 " model vdw 2.269 3.040 nonbonded pdb=" N GLU G 58 " pdb=" OE1 GLU G 58 " model vdw 2.293 3.120 ... (remaining 75041 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: 2.030 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.820 Find NCS groups from input model: 0.050 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 0.186 9074 Z= 0.232 Angle : 0.601 10.558 12292 Z= 0.336 Chirality : 0.040 0.165 1374 Planarity : 0.004 0.054 1560 Dihedral : 16.234 89.700 3238 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 0.21 % Allowed : 18.27 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.65 (0.26), residues: 1120 helix: 2.16 (0.27), residues: 375 sheet: -0.06 (0.32), residues: 280 loop : -0.66 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.014 0.001 TYR A 295 PHE 0.030 0.001 PHE A 186 TRP 0.015 0.001 TRP A 91 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9069) covalent geometry : angle 0.60034 (12282) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.12889 ( 10) hydrogen bonds : bond 0.16729 ( 446) hydrogen bonds : angle 6.90245 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.405 Fit side-chains REVERT: A 91 TRP cc_start: 0.7039 (OUTLIER) cc_final: 0.6097 (m-10) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.5512 time to fit residues: 92.3108 Evaluate side-chains 143 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain B residue 258 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 223 HIS B 75 GLN B 176 GLN B 220 GLN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091261 restraints weight = 11523.461| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.70 r_work: 0.2956 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 9074 Z= 0.341 Angle : 0.672 9.866 12292 Z= 0.353 Chirality : 0.049 0.179 1374 Planarity : 0.005 0.049 1560 Dihedral : 7.251 105.627 1255 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.70 % Allowed : 18.37 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.49 (0.26), residues: 1120 helix: 2.04 (0.27), residues: 374 sheet: -0.04 (0.32), residues: 273 loop : -0.84 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.022 0.002 TYR B 105 PHE 0.022 0.002 PHE A 276 TRP 0.013 0.002 TRP B 82 HIS 0.008 0.002 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00809 ( 9069) covalent geometry : angle 0.67155 (12282) SS BOND : bond 0.00489 ( 5) SS BOND : angle 1.31055 ( 10) hydrogen bonds : bond 0.04992 ( 446) hydrogen bonds : angle 5.18973 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.336 Fit side-chains REVERT: A 242 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7590 (tp) REVERT: A 271 SER cc_start: 0.8926 (p) cc_final: 0.8649 (t) REVERT: B 22 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.5817 (mtt180) REVERT: B 32 GLN cc_start: 0.8092 (mt0) cc_final: 0.7847 (mt0) REVERT: B 37 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8086 (mp) REVERT: B 100 VAL cc_start: 0.9147 (m) cc_final: 0.8913 (p) REVERT: B 258 ASP cc_start: 0.7597 (t0) cc_final: 0.6437 (t0) REVERT: C 276 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: C 317 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7787 (ttmm) REVERT: S 42 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8341 (mp0) REVERT: S 160 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7136 (ttm-80) outliers start: 35 outliers final: 9 residues processed: 174 average time/residue: 0.6047 time to fit residues: 111.7812 Evaluate side-chains 166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 266 HIS S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.146329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099142 restraints weight = 11809.156| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.80 r_work: 0.3114 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9074 Z= 0.134 Angle : 0.536 6.487 12292 Z= 0.281 Chirality : 0.042 0.154 1374 Planarity : 0.004 0.045 1560 Dihedral : 5.951 73.612 1251 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.80 % Allowed : 20.49 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.61 (0.26), residues: 1120 helix: 2.25 (0.27), residues: 377 sheet: -0.14 (0.31), residues: 275 loop : -0.78 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.014 0.001 TYR S 190 PHE 0.019 0.001 PHE A 186 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9069) covalent geometry : angle 0.53498 (12282) SS BOND : bond 0.00337 ( 5) SS BOND : angle 1.03641 ( 10) hydrogen bonds : bond 0.03798 ( 446) hydrogen bonds : angle 4.62256 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7484 (tpp) REVERT: A 92 ASP cc_start: 0.6439 (m-30) cc_final: 0.6113 (m-30) REVERT: A 227 LYS cc_start: 0.7446 (mtmm) cc_final: 0.7228 (mtmm) REVERT: A 271 SER cc_start: 0.8901 (p) cc_final: 0.8636 (t) REVERT: B 17 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7797 (pp30) REVERT: B 160 SER cc_start: 0.8632 (t) cc_final: 0.8322 (p) REVERT: B 258 ASP cc_start: 0.7433 (t0) cc_final: 0.7024 (t0) REVERT: B 303 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: C 276 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: C 302 TYR cc_start: 0.8641 (t80) cc_final: 0.8344 (t80) REVERT: S 42 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8184 (mp0) REVERT: S 160 ARG cc_start: 0.7564 (ttp80) cc_final: 0.6650 (ttm-80) outliers start: 36 outliers final: 11 residues processed: 177 average time/residue: 0.5995 time to fit residues: 112.6412 Evaluate side-chains 161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.144934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097351 restraints weight = 11992.020| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.82 r_work: 0.3099 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9074 Z= 0.175 Angle : 0.566 7.116 12292 Z= 0.293 Chirality : 0.043 0.157 1374 Planarity : 0.004 0.045 1560 Dihedral : 5.950 73.370 1251 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.12 % Allowed : 22.18 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.55 (0.26), residues: 1120 helix: 2.24 (0.27), residues: 377 sheet: -0.25 (0.30), residues: 285 loop : -0.81 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.014 0.001 TYR S 190 PHE 0.021 0.001 PHE A 186 TRP 0.010 0.001 TRP B 211 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9069) covalent geometry : angle 0.56528 (12282) SS BOND : bond 0.00269 ( 5) SS BOND : angle 1.18874 ( 10) hydrogen bonds : bond 0.03885 ( 446) hydrogen bonds : angle 4.59454 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.341 Fit side-chains REVERT: A 84 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7511 (tpp) REVERT: A 91 TRP cc_start: 0.6707 (OUTLIER) cc_final: 0.6459 (m-90) REVERT: A 215 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7733 (mp) REVERT: A 227 LYS cc_start: 0.7496 (mtmm) cc_final: 0.7155 (mtmm) REVERT: A 271 SER cc_start: 0.8955 (p) cc_final: 0.8668 (t) REVERT: B 17 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7837 (pp30) REVERT: B 22 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.5913 (mtt180) REVERT: B 46 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7271 (mtp85) REVERT: B 160 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 258 ASP cc_start: 0.7409 (t0) cc_final: 0.6305 (t0) REVERT: B 303 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: C 276 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: S 42 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8158 (mt-10) REVERT: S 160 ARG cc_start: 0.7591 (ttp80) cc_final: 0.6693 (ttm-80) outliers start: 39 outliers final: 15 residues processed: 169 average time/residue: 0.6155 time to fit residues: 110.5071 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 104 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 75 GLN S 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098842 restraints weight = 11871.407| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.81 r_work: 0.3123 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9074 Z= 0.143 Angle : 0.546 7.458 12292 Z= 0.282 Chirality : 0.042 0.159 1374 Planarity : 0.004 0.044 1560 Dihedral : 5.762 73.188 1251 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.65 % Allowed : 22.39 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.56 (0.26), residues: 1120 helix: 2.28 (0.27), residues: 377 sheet: -0.28 (0.30), residues: 284 loop : -0.80 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 38 TYR 0.013 0.001 TYR S 190 PHE 0.012 0.001 PHE C 189 TRP 0.009 0.001 TRP B 211 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9069) covalent geometry : angle 0.54553 (12282) SS BOND : bond 0.00312 ( 5) SS BOND : angle 1.09190 ( 10) hydrogen bonds : bond 0.03633 ( 446) hydrogen bonds : angle 4.43520 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6457 (pmm-80) REVERT: A 91 TRP cc_start: 0.6707 (OUTLIER) cc_final: 0.6444 (m-90) REVERT: A 215 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 271 SER cc_start: 0.8945 (p) cc_final: 0.8641 (t) REVERT: B 17 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7841 (pp30) REVERT: B 46 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7267 (mtp85) REVERT: B 160 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 258 ASP cc_start: 0.7611 (t0) cc_final: 0.6963 (t0) REVERT: B 303 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: C 276 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: S 42 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8213 (mp0) REVERT: S 76 LYS cc_start: 0.8423 (pttm) cc_final: 0.8167 (pmtt) REVERT: S 160 ARG cc_start: 0.7601 (ttp80) cc_final: 0.6701 (ttm-80) REVERT: S 220 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7559 (pm20) outliers start: 44 outliers final: 16 residues processed: 179 average time/residue: 0.6342 time to fit residues: 120.5049 Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 101 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 16 ASN B 75 GLN C 188 HIS S 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.150292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.103517 restraints weight = 11990.303| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.82 r_work: 0.3209 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9074 Z= 0.113 Angle : 0.528 8.123 12292 Z= 0.272 Chirality : 0.041 0.154 1374 Planarity : 0.004 0.043 1560 Dihedral : 5.552 72.982 1251 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.70 % Allowed : 24.08 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.58 (0.26), residues: 1120 helix: 2.27 (0.27), residues: 377 sheet: -0.22 (0.30), residues: 284 loop : -0.78 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 222 TYR 0.018 0.001 TYR C 287 PHE 0.011 0.001 PHE C 189 TRP 0.010 0.001 TRP B 211 HIS 0.002 0.000 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9069) covalent geometry : angle 0.52789 (12282) SS BOND : bond 0.00267 ( 5) SS BOND : angle 1.02152 ( 10) hydrogen bonds : bond 0.03369 ( 446) hydrogen bonds : angle 4.29227 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8065 (ttm) cc_final: 0.7485 (tpp) REVERT: A 91 TRP cc_start: 0.6732 (OUTLIER) cc_final: 0.6388 (m-90) REVERT: A 271 SER cc_start: 0.8965 (p) cc_final: 0.8642 (t) REVERT: B 17 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7913 (pp30) REVERT: B 46 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7366 (mtp85) REVERT: B 160 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8424 (p) REVERT: B 214 ARG cc_start: 0.8366 (tpp-160) cc_final: 0.8094 (tpp80) REVERT: C 276 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: S 43 LYS cc_start: 0.8814 (mppt) cc_final: 0.8603 (mppt) REVERT: S 76 LYS cc_start: 0.8370 (pttm) cc_final: 0.8114 (pmtt) REVERT: S 83 MET cc_start: 0.8337 (mtm) cc_final: 0.7997 (mtp) REVERT: S 160 ARG cc_start: 0.7660 (ttp80) cc_final: 0.6781 (ttm-80) REVERT: S 220 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7564 (pm20) outliers start: 35 outliers final: 15 residues processed: 179 average time/residue: 0.5981 time to fit residues: 113.9516 Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 75 GLN S 77 ASN S 142 GLN S 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099717 restraints weight = 11985.766| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.80 r_work: 0.3156 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9074 Z= 0.201 Angle : 0.587 8.374 12292 Z= 0.302 Chirality : 0.043 0.176 1374 Planarity : 0.004 0.047 1560 Dihedral : 5.860 72.704 1251 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.70 % Allowed : 24.82 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1120 helix: 2.16 (0.27), residues: 379 sheet: -0.28 (0.30), residues: 287 loop : -0.76 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.014 0.001 TYR S 190 PHE 0.014 0.001 PHE A 276 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9069) covalent geometry : angle 0.58634 (12282) SS BOND : bond 0.00370 ( 5) SS BOND : angle 1.09383 ( 10) hydrogen bonds : bond 0.03868 ( 446) hydrogen bonds : angle 4.50445 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.6410 (m-90) REVERT: A 112 GLN cc_start: 0.7246 (tp40) cc_final: 0.6832 (tp40) REVERT: A 271 SER cc_start: 0.8953 (p) cc_final: 0.8612 (t) REVERT: B 17 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7921 (pp30) REVERT: B 160 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8562 (p) REVERT: B 303 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: C 276 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: S 160 ARG cc_start: 0.7636 (ttp80) cc_final: 0.6758 (ttm-80) REVERT: S 220 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7623 (pm20) outliers start: 35 outliers final: 17 residues processed: 175 average time/residue: 0.6003 time to fit residues: 111.7474 Evaluate side-chains 175 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 98 optimal weight: 0.0870 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 15 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 75 GLN S 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099975 restraints weight = 11347.299| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.71 r_work: 0.3083 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9074 Z= 0.109 Angle : 0.547 9.049 12292 Z= 0.280 Chirality : 0.042 0.168 1374 Planarity : 0.003 0.044 1560 Dihedral : 5.513 72.378 1251 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.85 % Allowed : 25.55 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.58 (0.26), residues: 1120 helix: 2.22 (0.27), residues: 382 sheet: -0.17 (0.30), residues: 284 loop : -0.82 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.013 0.001 TYR S 190 PHE 0.010 0.001 PHE C 189 TRP 0.009 0.001 TRP B 339 HIS 0.005 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9069) covalent geometry : angle 0.54678 (12282) SS BOND : bond 0.00309 ( 5) SS BOND : angle 1.03265 ( 10) hydrogen bonds : bond 0.03262 ( 446) hydrogen bonds : angle 4.21840 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7402 (tpp) REVERT: A 86 ASN cc_start: 0.7630 (t0) cc_final: 0.7313 (t0) REVERT: A 91 TRP cc_start: 0.6611 (OUTLIER) cc_final: 0.6200 (m-90) REVERT: A 221 ASP cc_start: 0.8054 (p0) cc_final: 0.7683 (p0) REVERT: A 242 ILE cc_start: 0.7674 (tp) cc_final: 0.7263 (tp) REVERT: A 271 SER cc_start: 0.8990 (p) cc_final: 0.8645 (t) REVERT: B 17 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8009 (pp30) REVERT: B 160 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8449 (p) REVERT: B 258 ASP cc_start: 0.7455 (t0) cc_final: 0.6962 (t0) REVERT: C 276 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: S 83 MET cc_start: 0.8319 (mtm) cc_final: 0.8052 (mtp) REVERT: S 160 ARG cc_start: 0.7650 (ttp80) cc_final: 0.6791 (ttm-80) REVERT: S 220 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7609 (pm20) outliers start: 27 outliers final: 16 residues processed: 169 average time/residue: 0.5615 time to fit residues: 101.3723 Evaluate side-chains 171 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 75 GLN S 77 ASN S 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094266 restraints weight = 11461.160| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.71 r_work: 0.2994 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9074 Z= 0.216 Angle : 0.629 9.915 12292 Z= 0.320 Chirality : 0.044 0.185 1374 Planarity : 0.004 0.042 1560 Dihedral : 5.850 72.239 1251 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.38 % Allowed : 25.24 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.48 (0.26), residues: 1120 helix: 2.12 (0.27), residues: 380 sheet: -0.25 (0.30), residues: 286 loop : -0.83 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.014 0.002 TYR S 190 PHE 0.014 0.001 PHE A 276 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 9069) covalent geometry : angle 0.62875 (12282) SS BOND : bond 0.00394 ( 5) SS BOND : angle 1.11748 ( 10) hydrogen bonds : bond 0.03854 ( 446) hydrogen bonds : angle 4.52803 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7453 (tpp) REVERT: A 91 TRP cc_start: 0.6651 (OUTLIER) cc_final: 0.6327 (m-90) REVERT: A 242 ILE cc_start: 0.8006 (tp) cc_final: 0.7633 (tp) REVERT: A 271 SER cc_start: 0.8955 (p) cc_final: 0.8611 (t) REVERT: B 17 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7907 (pp30) REVERT: B 160 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8706 (p) REVERT: B 258 ASP cc_start: 0.7557 (t0) cc_final: 0.7004 (t0) REVERT: C 276 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: S 160 ARG cc_start: 0.7829 (ttp80) cc_final: 0.6968 (ttm-80) REVERT: S 220 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7584 (pm20) outliers start: 32 outliers final: 15 residues processed: 168 average time/residue: 0.6140 time to fit residues: 109.6347 Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN S 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101403 restraints weight = 11915.925| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.79 r_work: 0.3191 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9074 Z= 0.153 Angle : 0.610 10.692 12292 Z= 0.311 Chirality : 0.043 0.185 1374 Planarity : 0.004 0.039 1560 Dihedral : 5.792 72.151 1251 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.32 % Allowed : 26.50 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.46 (0.26), residues: 1120 helix: 2.09 (0.27), residues: 383 sheet: -0.23 (0.30), residues: 286 loop : -0.86 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 222 TYR 0.014 0.001 TYR S 190 PHE 0.012 0.001 PHE C 189 TRP 0.009 0.001 TRP S 47 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9069) covalent geometry : angle 0.60995 (12282) SS BOND : bond 0.00360 ( 5) SS BOND : angle 1.03124 ( 10) hydrogen bonds : bond 0.03577 ( 446) hydrogen bonds : angle 4.41550 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TRP cc_start: 0.6625 (OUTLIER) cc_final: 0.6262 (m-90) REVERT: A 242 ILE cc_start: 0.7929 (tp) cc_final: 0.7508 (tp) REVERT: A 271 SER cc_start: 0.8956 (p) cc_final: 0.8602 (t) REVERT: B 17 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7992 (pp30) REVERT: B 46 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7547 (mtp85) REVERT: B 160 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8604 (p) REVERT: B 258 ASP cc_start: 0.7534 (t0) cc_final: 0.6988 (t0) REVERT: C 276 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: S 160 ARG cc_start: 0.7711 (ttp80) cc_final: 0.6803 (ttm-80) REVERT: S 220 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7573 (pm20) outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 0.6039 time to fit residues: 102.1755 Evaluate side-chains 164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.6980 chunk 8 optimal weight: 0.0470 chunk 97 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104845 restraints weight = 11846.370| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.82 r_work: 0.3236 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9074 Z= 0.117 Angle : 0.583 10.170 12292 Z= 0.295 Chirality : 0.042 0.168 1374 Planarity : 0.004 0.039 1560 Dihedral : 5.525 71.822 1251 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.43 % Allowed : 26.40 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1120 helix: 2.23 (0.27), residues: 376 sheet: -0.15 (0.30), residues: 284 loop : -0.93 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 222 TYR 0.014 0.001 TYR S 190 PHE 0.010 0.001 PHE C 189 TRP 0.010 0.001 TRP B 211 HIS 0.002 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9069) covalent geometry : angle 0.58199 (12282) SS BOND : bond 0.00293 ( 5) SS BOND : angle 1.08500 ( 10) hydrogen bonds : bond 0.03286 ( 446) hydrogen bonds : angle 4.22767 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3672.84 seconds wall clock time: 63 minutes 32.48 seconds (3812.48 seconds total)