Starting phenix.real_space_refine on Mon Dec 30 00:06:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efl_28085/12_2024/8efl_28085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efl_28085/12_2024/8efl_28085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efl_28085/12_2024/8efl_28085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efl_28085/12_2024/8efl_28085.map" model { file = "/net/cci-nas-00/data/ceres_data/8efl_28085/12_2024/8efl_28085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efl_28085/12_2024/8efl_28085.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 Cl 6 4.86 5 C 7645 2.51 5 N 1908 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11750 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1788 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 183 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Link IDs: {'TRANS': 22} Chain: "R" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'CLR': 5, 'WH9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'CLR': 5, 'WH9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 7.24, per 1000 atoms: 0.62 Number of scatterers: 11750 At special positions: 0 Unit cell: (106.029, 116.739, 153.153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 6 17.00 S 98 16.00 O 2093 8.00 N 1908 7.00 C 7645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 15 sheets defined 49.7% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'R' and resid 66 through 98 Processing helix chain 'R' and resid 103 through 122 Processing helix chain 'R' and resid 122 through 133 removed outlier: 3.730A pdb=" N GLN R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.826A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.031A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 3.640A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.939A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.597A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.207A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 4.552A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.845A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.832A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.569A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.306A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.616A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'M' and resid 67 through 98 Processing helix chain 'M' and resid 103 through 121 Processing helix chain 'M' and resid 122 through 133 removed outlier: 3.535A pdb=" N GLN M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.689A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.807A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.745A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 264 removed outlier: 3.587A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 340 removed outlier: 3.745A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'F' and resid 333 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.806A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.298A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.738A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.734A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.791A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.740A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.398A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.711A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.672A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.672A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.761A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 703 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1808 1.30 - 1.43: 3148 1.43 - 1.56: 6917 1.56 - 1.69: 9 1.69 - 1.82: 151 Bond restraints: 12033 Sorted by residual: bond pdb=" C03 WH9 R 401 " pdb=" N01 WH9 R 401 " ideal model delta sigma weight residual 1.380 1.316 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C03 WH9 M 401 " pdb=" N01 WH9 M 401 " ideal model delta sigma weight residual 1.380 1.316 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C07 WH9 R 401 " pdb=" N02 WH9 R 401 " ideal model delta sigma weight residual 1.391 1.328 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C07 WH9 M 401 " pdb=" N02 WH9 M 401 " ideal model delta sigma weight residual 1.391 1.329 0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" C07 WH9 M 401 " pdb=" N01 WH9 M 401 " ideal model delta sigma weight residual 1.380 1.322 0.058 2.00e-02 2.50e+03 8.32e+00 ... (remaining 12028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 15520 1.77 - 3.54: 704 3.54 - 5.30: 121 5.30 - 7.07: 26 7.07 - 8.84: 8 Bond angle restraints: 16379 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 124.82 130.69 -5.87 1.78e+00 3.16e-01 1.09e+01 angle pdb=" N LEU R 123 " pdb=" CA LEU R 123 " pdb=" C LEU R 123 " ideal model delta sigma weight residual 109.81 116.89 -7.08 2.21e+00 2.05e-01 1.03e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 125.66 131.49 -5.83 1.85e+00 2.92e-01 9.92e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 128.11 -4.64 1.53e+00 4.27e-01 9.18e+00 ... (remaining 16374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 7238 14.15 - 28.29: 298 28.29 - 42.44: 60 42.44 - 56.58: 11 56.58 - 70.73: 2 Dihedral angle restraints: 7609 sinusoidal: 3381 harmonic: 4228 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ILE B 81 " pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 7606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1699 0.088 - 0.176: 168 0.176 - 0.264: 25 0.264 - 0.352: 8 0.352 - 0.440: 11 Chirality restraints: 1911 Sorted by residual: chirality pdb=" C14 CLR M 405 " pdb=" C13 CLR M 405 " pdb=" C15 CLR M 405 " pdb=" C8 CLR M 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1908 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO B 236 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 278 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ARG R 278 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG R 278 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG R 279 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 194 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.025 5.00e-02 4.00e+02 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2204 2.79 - 3.32: 10638 3.32 - 3.84: 19028 3.84 - 4.37: 21433 4.37 - 4.90: 38718 Nonbonded interactions: 92021 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.259 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.279 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.304 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.321 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.330 3.040 ... (remaining 92016 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 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'R' } 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.720 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12033 Z= 0.311 Angle : 0.867 8.841 16379 Z= 0.463 Chirality : 0.066 0.440 1911 Planarity : 0.006 0.075 1969 Dihedral : 8.532 70.730 4866 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1428 helix: 1.12 (0.17), residues: 664 sheet: 0.57 (0.30), residues: 283 loop : -1.19 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.005 0.001 HIS B 54 PHE 0.026 0.002 PHE A 189 TYR 0.024 0.002 TYR R 108 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.320 Fit side-chains REVERT: R 260 ARG cc_start: 0.7467 (tpt90) cc_final: 0.7009 (tpp80) REVERT: A 44 SER cc_start: 0.7619 (m) cc_final: 0.7127 (p) REVERT: A 309 ASP cc_start: 0.7249 (m-30) cc_final: 0.7039 (m-30) REVERT: B 150 ARG cc_start: 0.8430 (mmt-90) cc_final: 0.8179 (mpt180) REVERT: B 175 GLN cc_start: 0.7608 (mm110) cc_final: 0.7160 (mm110) REVERT: B 189 SER cc_start: 0.8838 (p) cc_final: 0.8480 (t) REVERT: E 167 LEU cc_start: 0.7827 (tp) cc_final: 0.7541 (tp) REVERT: M 266 MET cc_start: 0.5980 (tmt) cc_final: 0.5721 (ttp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2647 time to fit residues: 90.0466 Evaluate side-chains 160 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS B 35 ASN B 91 HIS B 155 ASN B 266 HIS B 293 ASN E 77 ASN E 180 GLN M 106 ASN M 330 ASN M 334 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12033 Z= 0.172 Angle : 0.489 6.837 16379 Z= 0.259 Chirality : 0.039 0.150 1911 Planarity : 0.004 0.055 1969 Dihedral : 5.990 64.757 2254 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.14 % Allowed : 6.72 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1428 helix: 2.61 (0.18), residues: 671 sheet: 0.57 (0.29), residues: 270 loop : -0.87 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.021 0.001 PHE A 189 TYR 0.019 0.001 TYR E 191 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.326 Fit side-chains REVERT: R 251 THR cc_start: 0.8990 (m) cc_final: 0.8741 (p) REVERT: R 310 ILE cc_start: 0.6318 (OUTLIER) cc_final: 0.5864 (tp) REVERT: A 309 ASP cc_start: 0.7330 (m-30) cc_final: 0.7041 (m-30) REVERT: A 350 ASP cc_start: 0.7460 (t0) cc_final: 0.7218 (m-30) REVERT: B 101 MET cc_start: 0.8916 (mtp) cc_final: 0.8663 (mtp) REVERT: B 161 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8920 (m) REVERT: B 175 GLN cc_start: 0.7595 (mm110) cc_final: 0.7379 (mm-40) REVERT: B 325 MET cc_start: 0.7466 (tpp) cc_final: 0.7103 (mmt) outliers start: 27 outliers final: 15 residues processed: 188 average time/residue: 0.2262 time to fit residues: 62.4848 Evaluate side-chains 160 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN B 75 GLN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12033 Z= 0.215 Angle : 0.506 6.749 16379 Z= 0.264 Chirality : 0.040 0.152 1911 Planarity : 0.004 0.046 1969 Dihedral : 6.231 61.421 2254 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.37 % Allowed : 8.70 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.21), residues: 1428 helix: 2.85 (0.18), residues: 669 sheet: 0.52 (0.29), residues: 280 loop : -0.65 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.019 0.002 PHE R 154 TYR 0.013 0.001 TYR E 191 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.450 Fit side-chains REVERT: R 251 THR cc_start: 0.8942 (m) cc_final: 0.8604 (p) REVERT: R 310 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6228 (tp) REVERT: A 240 MET cc_start: 0.3505 (OUTLIER) cc_final: 0.3224 (mtm) REVERT: A 309 ASP cc_start: 0.7352 (m-30) cc_final: 0.7150 (m-30) REVERT: A 350 ASP cc_start: 0.7720 (t0) cc_final: 0.7482 (m-30) REVERT: B 175 GLN cc_start: 0.7578 (mm110) cc_final: 0.7256 (mm-40) REVERT: B 262 MET cc_start: 0.7048 (ttm) cc_final: 0.6777 (ttm) REVERT: B 269 ILE cc_start: 0.7760 (mt) cc_final: 0.7560 (tp) REVERT: M 283 MET cc_start: 0.7493 (tpp) cc_final: 0.7189 (tpp) outliers start: 30 outliers final: 21 residues processed: 173 average time/residue: 0.2362 time to fit residues: 59.6863 Evaluate side-chains 159 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 349 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS M 111 ASN M 173 HIS M 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12033 Z= 0.315 Angle : 0.570 9.069 16379 Z= 0.293 Chirality : 0.042 0.149 1911 Planarity : 0.004 0.043 1969 Dihedral : 6.790 59.843 2254 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.40 % Allowed : 9.34 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.21), residues: 1428 helix: 2.71 (0.19), residues: 661 sheet: 0.42 (0.29), residues: 282 loop : -0.70 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS E 233 PHE 0.029 0.002 PHE R 154 TYR 0.023 0.002 TYR R 301 ARG 0.005 0.001 ARG R 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.225 Fit side-chains REVERT: R 251 THR cc_start: 0.8921 (m) cc_final: 0.8525 (p) REVERT: R 310 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.7077 (tp) REVERT: A 44 SER cc_start: 0.8060 (m) cc_final: 0.7566 (p) REVERT: A 240 MET cc_start: 0.4221 (OUTLIER) cc_final: 0.3977 (mtm) REVERT: B 175 GLN cc_start: 0.7726 (mm110) cc_final: 0.7512 (mp10) REVERT: B 262 MET cc_start: 0.7165 (ttm) cc_final: 0.6848 (ttm) REVERT: M 283 MET cc_start: 0.7681 (tpp) cc_final: 0.7299 (tpp) outliers start: 43 outliers final: 31 residues processed: 176 average time/residue: 0.2241 time to fit residues: 58.8794 Evaluate side-chains 163 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 222 THR Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12033 Z= 0.225 Angle : 0.507 7.333 16379 Z= 0.264 Chirality : 0.039 0.145 1911 Planarity : 0.004 0.050 1969 Dihedral : 6.447 58.653 2254 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.16 % Allowed : 10.68 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.22), residues: 1428 helix: 2.83 (0.19), residues: 663 sheet: 0.27 (0.29), residues: 282 loop : -0.63 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.018 0.001 PHE R 154 TYR 0.017 0.001 TYR E 94 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.377 Fit side-chains REVERT: R 251 THR cc_start: 0.8910 (m) cc_final: 0.8540 (p) REVERT: R 310 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7120 (tp) REVERT: A 44 SER cc_start: 0.7804 (m) cc_final: 0.7288 (p) REVERT: A 240 MET cc_start: 0.4590 (OUTLIER) cc_final: 0.4352 (mtm) REVERT: M 283 MET cc_start: 0.7621 (tpp) cc_final: 0.7269 (tpp) outliers start: 40 outliers final: 33 residues processed: 164 average time/residue: 0.2399 time to fit residues: 58.2719 Evaluate side-chains 157 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 131 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 321 HIS M 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12033 Z= 0.153 Angle : 0.459 6.070 16379 Z= 0.240 Chirality : 0.038 0.140 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.923 58.629 2254 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.93 % Allowed : 10.84 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.22), residues: 1428 helix: 2.96 (0.19), residues: 669 sheet: 0.17 (0.29), residues: 287 loop : -0.56 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.000 HIS C 44 PHE 0.014 0.001 PHE A 189 TYR 0.013 0.001 TYR M 151 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.386 Fit side-chains REVERT: R 251 THR cc_start: 0.8907 (m) cc_final: 0.8553 (p) REVERT: R 310 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7162 (tp) REVERT: R 333 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 44 SER cc_start: 0.7796 (m) cc_final: 0.7218 (p) REVERT: E 141 MET cc_start: 0.8428 (mmm) cc_final: 0.7542 (mmm) REVERT: M 283 MET cc_start: 0.7600 (tpp) cc_final: 0.7278 (tpp) REVERT: F 354 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6798 (m-80) outliers start: 37 outliers final: 27 residues processed: 162 average time/residue: 0.2293 time to fit residues: 54.7691 Evaluate side-chains 161 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 ASN E 180 GLN M 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12033 Z= 0.338 Angle : 0.573 9.329 16379 Z= 0.294 Chirality : 0.041 0.156 1911 Planarity : 0.004 0.043 1969 Dihedral : 6.580 59.212 2254 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.24 % Allowed : 11.00 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1428 helix: 2.75 (0.19), residues: 661 sheet: 0.10 (0.29), residues: 288 loop : -0.66 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 321 PHE 0.017 0.002 PHE A 189 TYR 0.023 0.002 TYR E 94 ARG 0.004 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.364 Fit side-chains REVERT: R 251 THR cc_start: 0.8949 (m) cc_final: 0.8537 (p) REVERT: R 266 MET cc_start: 0.6575 (tpp) cc_final: 0.6374 (tpp) REVERT: R 310 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7242 (tp) REVERT: A 44 SER cc_start: 0.7825 (m) cc_final: 0.7297 (p) REVERT: E 141 MET cc_start: 0.8520 (mmm) cc_final: 0.7649 (mmm) REVERT: E 193 MET cc_start: 0.8115 (ptm) cc_final: 0.7823 (ptt) REVERT: F 354 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7171 (m-80) outliers start: 41 outliers final: 35 residues processed: 166 average time/residue: 0.2346 time to fit residues: 57.0683 Evaluate side-chains 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12033 Z= 0.170 Angle : 0.475 6.974 16379 Z= 0.249 Chirality : 0.038 0.143 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.966 57.966 2254 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.37 % Allowed : 12.34 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.22), residues: 1428 helix: 2.92 (0.19), residues: 664 sheet: 0.13 (0.29), residues: 289 loop : -0.63 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.014 0.001 PHE E 240 TYR 0.012 0.001 TYR M 151 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.315 Fit side-chains REVERT: R 251 THR cc_start: 0.8925 (m) cc_final: 0.8537 (p) REVERT: R 310 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7310 (tp) REVERT: A 44 SER cc_start: 0.7848 (m) cc_final: 0.7322 (p) REVERT: A 327 THR cc_start: 0.7055 (m) cc_final: 0.6735 (p) REVERT: E 193 MET cc_start: 0.8040 (ptm) cc_final: 0.7767 (ptt) REVERT: M 283 MET cc_start: 0.7600 (tpp) cc_final: 0.7278 (tpp) REVERT: F 354 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7164 (m-80) outliers start: 30 outliers final: 26 residues processed: 156 average time/residue: 0.2236 time to fit residues: 51.6251 Evaluate side-chains 155 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12033 Z= 0.246 Angle : 0.515 7.360 16379 Z= 0.266 Chirality : 0.040 0.153 1911 Planarity : 0.003 0.039 1969 Dihedral : 6.101 59.698 2254 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.85 % Allowed : 12.18 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1428 helix: 2.85 (0.19), residues: 664 sheet: 0.12 (0.30), residues: 289 loop : -0.62 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.016 0.001 PHE E 240 TYR 0.015 0.001 TYR E 94 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 1.320 Fit side-chains REVERT: R 251 THR cc_start: 0.8934 (m) cc_final: 0.8531 (p) REVERT: R 310 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7394 (tp) REVERT: A 44 SER cc_start: 0.7707 (m) cc_final: 0.7193 (p) REVERT: A 327 THR cc_start: 0.7038 (m) cc_final: 0.6712 (p) REVERT: B 101 MET cc_start: 0.8956 (mtm) cc_final: 0.8348 (ptp) REVERT: E 141 MET cc_start: 0.8428 (mmm) cc_final: 0.7542 (mmm) REVERT: E 193 MET cc_start: 0.7997 (ptm) cc_final: 0.7722 (ptt) REVERT: M 283 MET cc_start: 0.7651 (tpp) cc_final: 0.7322 (tpp) REVERT: F 354 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7253 (m-80) outliers start: 36 outliers final: 34 residues processed: 159 average time/residue: 0.2329 time to fit residues: 54.8088 Evaluate side-chains 165 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12033 Z= 0.162 Angle : 0.468 6.336 16379 Z= 0.245 Chirality : 0.038 0.140 1911 Planarity : 0.003 0.037 1969 Dihedral : 5.702 55.760 2254 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.61 % Allowed : 12.58 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.22), residues: 1428 helix: 2.98 (0.19), residues: 664 sheet: 0.16 (0.30), residues: 289 loop : -0.56 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS R 321 PHE 0.014 0.001 PHE E 240 TYR 0.012 0.001 TYR M 151 ARG 0.002 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.277 Fit side-chains REVERT: R 251 THR cc_start: 0.9021 (m) cc_final: 0.8669 (p) REVERT: R 310 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7238 (tp) REVERT: A 44 SER cc_start: 0.7805 (m) cc_final: 0.7277 (p) REVERT: A 209 LYS cc_start: 0.8440 (pttt) cc_final: 0.8178 (ptmt) REVERT: A 327 THR cc_start: 0.7100 (m) cc_final: 0.6766 (p) REVERT: B 101 MET cc_start: 0.8926 (mtm) cc_final: 0.8463 (ptp) REVERT: E 141 MET cc_start: 0.8288 (mmm) cc_final: 0.7463 (mmm) REVERT: E 193 MET cc_start: 0.7978 (ptm) cc_final: 0.7738 (ptt) REVERT: M 283 MET cc_start: 0.7570 (tpp) cc_final: 0.7247 (tpp) REVERT: F 354 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7159 (m-80) outliers start: 33 outliers final: 30 residues processed: 161 average time/residue: 0.2375 time to fit residues: 56.4279 Evaluate side-chains 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.171674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131219 restraints weight = 12332.848| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.41 r_work: 0.3012 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12033 Z= 0.249 Angle : 0.518 7.351 16379 Z= 0.267 Chirality : 0.040 0.148 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.981 58.581 2254 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.69 % Allowed : 12.74 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.22), residues: 1428 helix: 2.88 (0.19), residues: 664 sheet: 0.10 (0.29), residues: 289 loop : -0.57 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS C 44 PHE 0.016 0.001 PHE E 240 TYR 0.016 0.001 TYR E 94 ARG 0.003 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.97 seconds wall clock time: 45 minutes 42.75 seconds (2742.75 seconds total)