Starting phenix.real_space_refine on Wed Aug 5 13:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjq_39346/08_2026/8yjq_39346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjq_39346/08_2026/8yjq_39346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yjq_39346/08_2026/8yjq_39346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjq_39346/08_2026/8yjq_39346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yjq_39346/08_2026/8yjq_39346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjq_39346/08_2026/8yjq_39346.map" } resolution = 3.51 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 300 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 63 5.16 5 C 6024 2.51 5 N 1652 2.21 5 O 2059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9856 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2769 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "J" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 576 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Time building chain proxies: 1.81, per 1000 atoms: 0.18 Number of scatterers: 9856 At special positions: 0 Unit cell: (106.24, 104.58, 104.58, 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) S 63 16.00 P 58 15.00 O 2059 8.00 N 1652 7.00 C 6024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " 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: 0.82 Conformation dependent library (CDL) restraints added in 329.6 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 28.3% alpha, 26.0% beta 14 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'D' and resid 5 through 12 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.679A pdb=" N ALA D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.630A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 removed outlier: 3.744A pdb=" N VAL D 131 " --> pdb=" O LYS D 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 128 through 131' Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.564A pdb=" N GLU D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 149 removed outlier: 3.819A pdb=" N LEU D 145 " --> pdb=" O CYS D 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 147 " --> pdb=" O HIS D 143 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.595A pdb=" N ALA D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.950A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 219 through 230 removed outlier: 4.133A pdb=" N ASP D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.668A pdb=" N VAL D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.702A pdb=" N VAL D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 261' Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 304 through 310 removed outlier: 3.744A pdb=" N LYS D 308 " --> pdb=" O GLU D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.609A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.646A pdb=" N ASP D 342 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.600A pdb=" N ALA A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.902A pdb=" N ARG A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.734A pdb=" N ALA A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.737A pdb=" N PHE A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'C' and resid 9 through 17 removed outlier: 3.657A pdb=" N LEU C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.558A pdb=" N VAL B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 216 removed outlier: 3.852A pdb=" N PHE B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.572A pdb=" N ALA D 175 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 31 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL D 84 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 33 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 336 through 337 removed outlier: 4.007A pdb=" N THR D 336 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 345 through 349 removed outlier: 4.409A pdb=" N LYS D 345 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN C 125 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.601A pdb=" N THR A 59 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 4 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 100 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 99 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C 166 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 71 removed outlier: 3.793A pdb=" N MET A 68 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 26 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 251 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 235 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.518A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 180 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 111 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE B 2 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.937A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 205 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 66 through 71 removed outlier: 7.284A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.647A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2964 1.34 - 1.46: 2398 1.46 - 1.58: 4546 1.58 - 1.71: 113 1.71 - 1.83: 102 Bond restraints: 10123 Sorted by residual: bond pdb=" C3' DT J 5 " pdb=" C2' DT J 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C1' DT J 17 " pdb=" N1 DT J 17 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" CA ALA D 176 " pdb=" CB ALA D 176 " ideal model delta sigma weight residual 1.524 1.486 0.037 1.30e-02 5.92e+03 8.14e+00 bond pdb=" C3' DT J 12 " pdb=" C2' DT J 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.92e+00 bond pdb=" N PHE D 85 " pdb=" CA PHE D 85 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.17e-02 7.31e+03 7.70e+00 ... (remaining 10118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 13455 2.49 - 4.99: 366 4.99 - 7.48: 58 7.48 - 9.98: 23 9.98 - 12.47: 4 Bond angle restraints: 13906 Sorted by residual: angle pdb=" C ALA A 242 " pdb=" N ASP A 243 " pdb=" CA ASP A 243 " ideal model delta sigma weight residual 121.54 134.01 -12.47 1.91e+00 2.74e-01 4.26e+01 angle pdb=" C LYS D 314 " pdb=" N GLN D 315 " pdb=" CA GLN D 315 " ideal model delta sigma weight residual 122.36 129.01 -6.65 1.42e+00 4.96e-01 2.20e+01 angle pdb=" C ALA C 242 " pdb=" N ASP C 243 " pdb=" CA ASP C 243 " ideal model delta sigma weight residual 122.08 128.51 -6.43 1.47e+00 4.63e-01 1.91e+01 angle pdb=" N3 DT E 11 " pdb=" C4 DT E 11 " pdb=" O4 DT E 11 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 13901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5046 17.91 - 35.82: 722 35.82 - 53.73: 285 53.73 - 71.64: 64 71.64 - 89.55: 12 Dihedral angle restraints: 6129 sinusoidal: 2883 harmonic: 3246 Sorted by residual: dihedral pdb=" CA MET C 139 " pdb=" C MET C 139 " pdb=" N PRO C 140 " pdb=" CA PRO C 140 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PRO D 81 " pdb=" C PRO D 81 " pdb=" N VAL D 82 " pdb=" CA VAL D 82 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ILE D 33 " pdb=" C ILE D 33 " pdb=" N ASP D 34 " pdb=" CA ASP D 34 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1268 0.061 - 0.121: 278 0.121 - 0.182: 41 0.182 - 0.243: 9 0.243 - 0.303: 4 Chirality restraints: 1600 Sorted by residual: chirality pdb=" CB ILE B 128 " pdb=" CA ILE B 128 " pdb=" CG1 ILE B 128 " pdb=" CG2 ILE B 128 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE A 128 " pdb=" CA ILE A 128 " pdb=" CG1 ILE A 128 " pdb=" CG2 ILE A 128 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ASP A 243 " pdb=" N ASP A 243 " pdb=" C ASP A 243 " pdb=" CB ASP A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1597 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 207 " -0.015 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE B 207 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 207 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 207 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE B 207 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 207 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 207 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 128 " -0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO B 129 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 220 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.045 5.00e-02 4.00e+02 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3210 2.87 - 3.38: 8198 3.38 - 3.89: 17220 3.89 - 4.39: 19050 4.39 - 4.90: 32017 Nonbonded interactions: 79695 Sorted by model distance: nonbonded pdb=" OD2 ASP A 41 " pdb=" OG SER A 43 " model vdw 2.366 3.040 nonbonded pdb=" OE1 GLU D 158 " pdb=" OH TYR D 234 " model vdw 2.378 3.040 nonbonded pdb=" OG SER A 222 " pdb=" O THR A 224 " model vdw 2.379 3.040 nonbonded pdb=" OG SER A 141 " pdb=" O SER A 222 " model vdw 2.392 3.040 nonbonded pdb=" ND2 ASN D 302 " pdb=" OE1 GLU D 305 " model vdw 2.433 3.120 ... (remaining 79690 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 'A' selection = chain 'B' selection = (chain 'C' and resid 1 through 254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.120 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 0.063 10126 Z= 0.332 Angle : 1.010 12.473 13912 Z= 0.608 Chirality : 0.056 0.303 1600 Planarity : 0.007 0.081 1590 Dihedral : 19.575 89.548 4014 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.20), residues: 1107 helix: -4.24 (0.13), residues: 289 sheet: -1.66 (0.27), residues: 327 loop : -1.82 (0.23), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 239 TYR 0.054 0.003 TYR A 249 PHE 0.052 0.003 PHE B 207 TRP 0.021 0.002 TRP A 28 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.33 (10123) covalent geometry : angle 1.01014 / 0.61 (13906) SS BOND : bond 0.00272 / 0.15 ( 3) SS BOND : angle 0.60753 / 0.44 ( 6) hydrogen bonds : bond 0.27218 / 18.21 ( 416) hydrogen bonds : angle 10.98781 / 7.65 ( 1142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.365 Fit side-chains REVERT: D 21 ASN cc_start: 0.7921 (m110) cc_final: 0.7675 (m-40) REVERT: D 189 VAL cc_start: 0.9002 (t) cc_final: 0.8627 (p) REVERT: A 125 GLN cc_start: 0.7939 (pp30) cc_final: 0.7665 (pp30) REVERT: B 59 THR cc_start: 0.8043 (m) cc_final: 0.7586 (p) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0897 time to fit residues: 19.0858 Evaluate side-chains 107 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 ASN D 205 GLN A 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.157959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125735 restraints weight = 14221.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130117 restraints weight = 10284.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.131077 restraints weight = 6098.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132440 restraints weight = 5276.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.132604 restraints weight = 4451.801| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10126 Z= 0.182 Angle : 0.652 8.891 13912 Z= 0.354 Chirality : 0.047 0.205 1600 Planarity : 0.005 0.053 1590 Dihedral : 20.778 82.230 1871 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.24 % Allowed : 9.18 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.22), residues: 1107 helix: -2.40 (0.23), residues: 305 sheet: -1.70 (0.26), residues: 326 loop : -1.49 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 192 TYR 0.017 0.002 TYR D 26 PHE 0.026 0.002 PHE D 207 TRP 0.009 0.001 TRP D 274 HIS 0.004 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (10123) covalent geometry : angle 0.65167 / 0.35 (13906) SS BOND : bond 0.00159 / 0.10 ( 3) SS BOND : angle 0.50573 / 0.26 ( 6) hydrogen bonds : bond 0.05279 / 3.67 ( 416) hydrogen bonds : angle 7.20043 / 4.97 ( 1142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.371 Fit side-chains REVERT: B 75 MET cc_start: 0.8872 (tpp) cc_final: 0.7963 (ttt) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.0925 time to fit residues: 16.3290 Evaluate side-chains 104 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 HIS C 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.158455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.124426 restraints weight = 13960.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129090 restraints weight = 8340.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129970 restraints weight = 5740.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130159 restraints weight = 4808.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130740 restraints weight = 4671.477| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10126 Z= 0.183 Angle : 0.599 7.168 13912 Z= 0.325 Chirality : 0.045 0.151 1600 Planarity : 0.004 0.046 1590 Dihedral : 20.886 82.512 1871 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.65 % Allowed : 12.18 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.23), residues: 1107 helix: -1.23 (0.27), residues: 307 sheet: -1.84 (0.26), residues: 318 loop : -1.22 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 239 TYR 0.017 0.002 TYR D 26 PHE 0.020 0.002 PHE D 207 TRP 0.008 0.001 TRP D 274 HIS 0.004 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (10123) covalent geometry : angle 0.59881 / 0.32 (13906) SS BOND : bond 0.00245 / 0.13 ( 3) SS BOND : angle 0.63820 / 0.32 ( 6) hydrogen bonds : bond 0.04675 / 3.14 ( 416) hydrogen bonds : angle 6.37599 / 4.39 ( 1142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.358 Fit side-chains REVERT: D 239 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8095 (mmm160) REVERT: A 16 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8714 (mm) REVERT: A 146 ARG cc_start: 0.7778 (ptp90) cc_final: 0.7552 (ptp-170) REVERT: B 75 MET cc_start: 0.8832 (tpp) cc_final: 0.8104 (ttt) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 0.1001 time to fit residues: 16.2909 Evaluate side-chains 100 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN C 108 GLN C 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.157702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.123376 restraints weight = 14086.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127554 restraints weight = 7702.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.130296 restraints weight = 5216.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132053 restraints weight = 4000.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133233 restraints weight = 3344.778| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10126 Z= 0.167 Angle : 0.565 6.208 13912 Z= 0.309 Chirality : 0.045 0.150 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.760 82.716 1871 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 13.42 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.24), residues: 1107 helix: -0.67 (0.28), residues: 309 sheet: -1.96 (0.25), residues: 331 loop : -1.00 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 73 TYR 0.021 0.002 TYR D 83 PHE 0.017 0.001 PHE D 207 TRP 0.008 0.001 TRP D 274 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (10123) covalent geometry : angle 0.56537 / 0.31 (13906) SS BOND : bond 0.00190 / 0.11 ( 3) SS BOND : angle 0.48285 / 0.24 ( 6) hydrogen bonds : bond 0.03912 / 2.68 ( 416) hydrogen bonds : angle 6.15226 / 4.25 ( 1142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.373 Fit side-chains REVERT: A 38 GLN cc_start: 0.7297 (mp10) cc_final: 0.7071 (mp10) REVERT: A 146 ARG cc_start: 0.7678 (ptp90) cc_final: 0.7470 (ptp-170) REVERT: B 75 MET cc_start: 0.8811 (tpp) cc_final: 0.8153 (ttt) outliers start: 17 outliers final: 11 residues processed: 110 average time/residue: 0.1182 time to fit residues: 17.9149 Evaluate side-chains 103 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 27 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN C 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.158738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124606 restraints weight = 14061.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128856 restraints weight = 7592.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.131627 restraints weight = 5107.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133435 restraints weight = 3893.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.134566 restraints weight = 3236.165| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10126 Z= 0.134 Angle : 0.534 5.723 13912 Z= 0.292 Chirality : 0.043 0.147 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.696 82.494 1871 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.96 % Allowed : 14.45 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.24), residues: 1107 helix: -0.30 (0.29), residues: 309 sheet: -1.91 (0.25), residues: 337 loop : -0.83 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 29 TYR 0.014 0.001 TYR D 26 PHE 0.015 0.001 PHE D 207 TRP 0.008 0.001 TRP D 274 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10123) covalent geometry : angle 0.53405 / 0.29 (13906) SS BOND : bond 0.00171 / 0.09 ( 3) SS BOND : angle 0.38758 / 0.21 ( 6) hydrogen bonds : bond 0.03672 / 2.47 ( 416) hydrogen bonds : angle 5.90507 / 4.07 ( 1142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.358 Fit side-chains REVERT: D 86 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: D 148 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.5149 (mmt) REVERT: C 115 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: B 75 MET cc_start: 0.8811 (tpp) cc_final: 0.8118 (ttt) outliers start: 19 outliers final: 9 residues processed: 112 average time/residue: 0.1060 time to fit residues: 16.7915 Evaluate side-chains 105 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 92 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 ASN C 38 GLN C 108 GLN C 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.157716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123449 restraints weight = 14016.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127760 restraints weight = 7553.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.130455 restraints weight = 5061.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132261 restraints weight = 3880.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.133226 restraints weight = 3220.034| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10126 Z= 0.146 Angle : 0.535 5.942 13912 Z= 0.292 Chirality : 0.043 0.143 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.654 82.040 1871 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.06 % Allowed : 15.89 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.24), residues: 1107 helix: -0.10 (0.29), residues: 314 sheet: -1.84 (0.25), residues: 337 loop : -0.70 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 29 TYR 0.015 0.001 TYR D 26 PHE 0.014 0.001 PHE D 207 TRP 0.007 0.001 TRP D 274 HIS 0.005 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (10123) covalent geometry : angle 0.53512 / 0.29 (13906) SS BOND : bond 0.00176 / 0.10 ( 3) SS BOND : angle 0.44878 / 0.23 ( 6) hydrogen bonds : bond 0.03548 / 2.37 ( 416) hydrogen bonds : angle 5.72031 / 3.94 ( 1142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.365 Fit side-chains REVERT: D 86 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6652 (m-30) REVERT: D 148 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.5307 (mmt) REVERT: C 115 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: B 75 MET cc_start: 0.8820 (tpp) cc_final: 0.8105 (ttt) outliers start: 20 outliers final: 9 residues processed: 113 average time/residue: 0.0980 time to fit residues: 15.8455 Evaluate side-chains 107 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 229 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.157367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122989 restraints weight = 13963.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127256 restraints weight = 7553.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.129931 restraints weight = 5066.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131769 restraints weight = 3882.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.132926 restraints weight = 3226.335| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10126 Z= 0.156 Angle : 0.538 5.978 13912 Z= 0.293 Chirality : 0.043 0.143 1600 Planarity : 0.003 0.042 1590 Dihedral : 20.597 81.861 1871 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.75 % Allowed : 16.62 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1107 helix: 0.01 (0.30), residues: 314 sheet: -1.80 (0.25), residues: 331 loop : -0.63 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 29 TYR 0.015 0.001 TYR D 26 PHE 0.014 0.001 PHE D 207 TRP 0.007 0.001 TRP D 274 HIS 0.005 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10123) covalent geometry : angle 0.53758 / 0.29 (13906) SS BOND : bond 0.00179 / 0.10 ( 3) SS BOND : angle 0.40480 / 0.22 ( 6) hydrogen bonds : bond 0.03506 / 2.31 ( 416) hydrogen bonds : angle 5.69570 / 3.92 ( 1142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.369 Fit side-chains REVERT: D 86 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: D 148 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.5407 (mmt) REVERT: C 115 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7359 (mt-10) outliers start: 17 outliers final: 10 residues processed: 105 average time/residue: 0.0968 time to fit residues: 14.3600 Evaluate side-chains 108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 229 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 91 optimal weight: 0.0670 chunk 102 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.156987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122640 restraints weight = 13817.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.126850 restraints weight = 7491.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129594 restraints weight = 5051.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131141 restraints weight = 3855.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132438 restraints weight = 3242.521| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10126 Z= 0.152 Angle : 0.539 6.073 13912 Z= 0.293 Chirality : 0.043 0.143 1600 Planarity : 0.003 0.042 1590 Dihedral : 20.528 81.709 1871 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.86 % Allowed : 16.62 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.25), residues: 1107 helix: 0.15 (0.30), residues: 312 sheet: -1.81 (0.25), residues: 335 loop : -0.57 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.015 0.001 TYR D 26 PHE 0.014 0.001 PHE D 207 TRP 0.006 0.001 TRP C 28 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (10123) covalent geometry : angle 0.53882 / 0.29 (13906) SS BOND : bond 0.00181 / 0.10 ( 3) SS BOND : angle 0.41668 / 0.22 ( 6) hydrogen bonds : bond 0.03437 / 2.25 ( 416) hydrogen bonds : angle 5.66092 / 3.89 ( 1142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.272 Fit side-chains REVERT: D 86 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.6636 (m-30) REVERT: D 148 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.5563 (mmt) REVERT: C 115 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: B 198 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7336 (mp0) outliers start: 18 outliers final: 11 residues processed: 109 average time/residue: 0.1066 time to fit residues: 16.2475 Evaluate side-chains 113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.153583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.118785 restraints weight = 13837.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.122926 restraints weight = 7584.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125665 restraints weight = 5103.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.127425 restraints weight = 3918.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128577 restraints weight = 3265.986| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10126 Z= 0.219 Angle : 0.595 6.480 13912 Z= 0.318 Chirality : 0.045 0.170 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.519 81.156 1871 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.65 % Allowed : 17.13 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.25), residues: 1107 helix: 0.10 (0.30), residues: 309 sheet: -1.85 (0.25), residues: 338 loop : -0.69 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 64 TYR 0.019 0.002 TYR D 26 PHE 0.016 0.002 PHE D 207 TRP 0.006 0.001 TRP D 274 HIS 0.005 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (10123) covalent geometry : angle 0.59478 / 0.32 (13906) SS BOND : bond 0.00222 / 0.12 ( 3) SS BOND : angle 0.58869 / 0.32 ( 6) hydrogen bonds : bond 0.03614 / 2.35 ( 416) hydrogen bonds : angle 5.82514 / 3.99 ( 1142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.270 Fit side-chains REVERT: D 86 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.6793 (m-30) REVERT: D 148 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.5802 (mmt) REVERT: C 115 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: B 198 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7397 (mp0) outliers start: 16 outliers final: 11 residues processed: 110 average time/residue: 0.0947 time to fit residues: 14.7261 Evaluate side-chains 110 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.155783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.121251 restraints weight = 13874.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125585 restraints weight = 7526.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.128334 restraints weight = 5020.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.130129 restraints weight = 3819.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.131179 restraints weight = 3183.077| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10126 Z= 0.150 Angle : 0.563 7.325 13912 Z= 0.303 Chirality : 0.044 0.173 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.514 81.476 1871 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.65 % Allowed : 17.96 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1107 helix: 0.23 (0.30), residues: 308 sheet: -1.84 (0.25), residues: 335 loop : -0.65 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 64 TYR 0.015 0.001 TYR D 26 PHE 0.015 0.001 PHE D 207 TRP 0.006 0.001 TRP C 28 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10123) covalent geometry : angle 0.56298 / 0.30 (13906) SS BOND : bond 0.00152 / 0.08 ( 3) SS BOND : angle 0.39821 / 0.22 ( 6) hydrogen bonds : bond 0.03386 / 2.19 ( 416) hydrogen bonds : angle 5.74188 / 3.94 ( 1142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.261 Fit side-chains REVERT: D 86 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: D 148 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.5772 (mmt) REVERT: C 115 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: C 201 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7171 (pt0) REVERT: B 198 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7373 (mp0) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.0816 time to fit residues: 13.1147 Evaluate side-chains 114 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.0070 chunk 93 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.156448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122157 restraints weight = 13984.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126482 restraints weight = 7512.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129276 restraints weight = 5002.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.131011 restraints weight = 3805.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132068 restraints weight = 3170.154| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10126 Z= 0.141 Angle : 0.565 11.370 13912 Z= 0.302 Chirality : 0.044 0.194 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.485 81.300 1871 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 18.27 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.25), residues: 1107 helix: 0.28 (0.30), residues: 308 sheet: -1.80 (0.25), residues: 338 loop : -0.60 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 64 TYR 0.014 0.001 TYR D 26 PHE 0.014 0.001 PHE D 207 TRP 0.006 0.001 TRP D 274 HIS 0.002 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10123) covalent geometry : angle 0.56514 / 0.30 (13906) SS BOND : bond 0.00135 / 0.07 ( 3) SS BOND : angle 0.51629 / 0.29 ( 6) hydrogen bonds : bond 0.03396 / 2.19 ( 416) hydrogen bonds : angle 5.67389 / 3.89 ( 1142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1651.79 seconds wall clock time: 29 minutes 15.14 seconds (1755.14 seconds total)