Starting phenix.real_space_refine on Thu Jul 2 19:58:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjq_39346/07_2026/8yjq_39346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjq_39346/07_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_39346/07_2026/8yjq_39346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjq_39346/07_2026/8yjq_39346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yjq_39346/07_2026/8yjq_39346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjq_39346/07_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-dev-6108/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: 2.14, per 1000 atoms: 0.22 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: 0.87 Conformation dependent library (CDL) restraints added in 355.3 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: 1.13 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: 1.10 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.750 Find NCS groups from input model: 0.130 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- 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 : 1.009 12.473 13912 Z= 0.607 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 1.00922 / 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 : 0.216 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: 0.0854 time to fit residues: 18.1010 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 : 0.345 ------------------------------------------------------------------------------- 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: 9.9990 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: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.157599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124376 restraints weight = 14219.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130445 restraints weight = 8441.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.131152 restraints weight = 4962.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.130966 restraints weight = 4550.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131137 restraints weight = 4383.241| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10126 Z= 0.190 Angle : 0.659 8.763 13912 Z= 0.360 Chirality : 0.047 0.207 1600 Planarity : 0.005 0.053 1590 Dihedral : 20.810 82.444 1871 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.85 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: -2.88 (0.22), residues: 1107 helix: -2.42 (0.22), residues: 305 sheet: -1.69 (0.26), residues: 326 loop : -1.49 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 192 TYR 0.017 0.002 TYR D 26 PHE 0.024 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 0.00409 / 0.19 (10123) covalent geometry : angle 0.65910 / 0.36 (13906) SS BOND : bond 0.00168 / 0.10 ( 3) SS BOND : angle 0.42248 / 0.22 ( 6) hydrogen bonds : bond 0.05358 / 3.72 ( 416) hydrogen bonds : angle 7.19737 / 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 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.358 Fit side-chains REVERT: B 75 MET cc_start: 0.8877 (tpp) cc_final: 0.8025 (ttt) outliers start: 12 outliers final: 7 residues processed: 121 average time/residue: 0.0958 time to fit residues: 16.7445 Evaluate side-chains 103 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 0.8980 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.159703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.125755 restraints weight = 13995.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130126 restraints weight = 8351.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.131170 restraints weight = 5825.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131597 restraints weight = 4848.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.131808 restraints weight = 4681.899| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10126 Z= 0.160 Angle : 0.580 6.846 13912 Z= 0.316 Chirality : 0.045 0.148 1600 Planarity : 0.004 0.046 1590 Dihedral : 20.903 82.594 1871 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.55 % Allowed : 11.87 % Favored : 86.58 % 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: -2.22 (0.23), residues: 1107 helix: -1.22 (0.27), residues: 307 sheet: -1.76 (0.26), residues: 318 loop : -1.23 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 239 TYR 0.015 0.001 TYR D 26 PHE 0.019 0.001 PHE D 207 TRP 0.008 0.001 TRP D 274 HIS 0.003 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (10123) covalent geometry : angle 0.58003 / 0.32 (13906) SS BOND : bond 0.00182 / 0.10 ( 3) SS BOND : angle 0.59476 / 0.31 ( 6) hydrogen bonds : bond 0.04669 / 3.14 ( 416) hydrogen bonds : angle 6.37642 / 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 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.358 Fit side-chains REVERT: D 239 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8075 (mmm160) REVERT: A 146 ARG cc_start: 0.7746 (ptp90) cc_final: 0.7535 (ptp-170) REVERT: B 75 MET cc_start: 0.8830 (tpp) cc_final: 0.8080 (ttt) outliers start: 15 outliers final: 8 residues processed: 113 average time/residue: 0.1002 time to fit residues: 15.9277 Evaluate side-chains 103 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 206 THR 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: 0.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.157971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123678 restraints weight = 14093.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127966 restraints weight = 7673.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.130679 restraints weight = 5167.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132469 restraints weight = 3963.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.133645 restraints weight = 3298.588| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10126 Z= 0.172 Angle : 0.567 6.069 13912 Z= 0.309 Chirality : 0.045 0.146 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.800 82.911 1871 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.86 % Allowed : 13.00 % Favored : 85.14 % 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: -1.94 (0.24), residues: 1107 helix: -0.70 (0.28), residues: 306 sheet: -1.90 (0.25), residues: 330 loop : -0.98 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 192 TYR 0.017 0.001 TYR D 26 PHE 0.017 0.001 PHE D 207 TRP 0.007 0.001 TRP D 274 HIS 0.008 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (10123) covalent geometry : angle 0.56751 / 0.31 (13906) SS BOND : bond 0.00196 / 0.11 ( 3) SS BOND : angle 0.48654 / 0.24 ( 6) hydrogen bonds : bond 0.03939 / 2.70 ( 416) hydrogen bonds : angle 6.12419 / 4.22 ( 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 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.355 Fit side-chains REVERT: A 38 GLN cc_start: 0.7272 (mp10) cc_final: 0.7062 (mp10) REVERT: A 146 ARG cc_start: 0.7689 (ptp90) cc_final: 0.7480 (ptp-170) REVERT: C 115 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: B 75 MET cc_start: 0.8813 (tpp) cc_final: 0.8158 (ttt) outliers start: 18 outliers final: 10 residues processed: 113 average time/residue: 0.1034 time to fit residues: 16.5325 Evaluate side-chains 106 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 27 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 24 optimal weight: 0.0870 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.159504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.125444 restraints weight = 14073.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129727 restraints weight = 7613.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.132488 restraints weight = 5100.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.134114 restraints weight = 3895.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.135385 restraints weight = 3269.595| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2520 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= 0.126 Angle : 0.529 5.846 13912 Z= 0.290 Chirality : 0.043 0.159 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.733 82.733 1871 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.17 % Allowed : 14.14 % Favored : 83.69 % 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: -1.66 (0.24), residues: 1107 helix: -0.29 (0.29), residues: 307 sheet: -1.90 (0.25), residues: 339 loop : -0.79 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 239 TYR 0.013 0.001 TYR D 26 PHE 0.014 0.001 PHE D 207 TRP 0.007 0.001 TRP D 274 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10123) covalent geometry : angle 0.52908 / 0.29 (13906) SS BOND : bond 0.00119 / 0.07 ( 3) SS BOND : angle 0.35969 / 0.20 ( 6) hydrogen bonds : bond 0.03702 / 2.48 ( 416) hydrogen bonds : angle 5.90846 / 4.08 ( 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 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.357 Fit side-chains REVERT: D 86 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: D 148 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.4979 (mmt) REVERT: C 115 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: B 75 MET cc_start: 0.8797 (tpp) cc_final: 0.8104 (ttt) outliers start: 21 outliers final: 10 residues processed: 114 average time/residue: 0.1074 time to fit residues: 16.8575 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 : 0.308 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 5 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN B 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.159435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125363 restraints weight = 14049.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.129665 restraints weight = 7589.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.132409 restraints weight = 5076.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.134090 restraints weight = 3869.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.135373 restraints weight = 3229.140| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10126 Z= 0.123 Angle : 0.525 5.916 13912 Z= 0.288 Chirality : 0.043 0.148 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.674 82.588 1871 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 15.38 % Favored : 82.87 % 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: -0.06 (0.30), residues: 309 sheet: -1.87 (0.25), residues: 341 loop : -0.70 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 64 TYR 0.013 0.001 TYR D 26 PHE 0.013 0.001 PHE D 207 TRP 0.006 0.001 TRP C 28 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10123) covalent geometry : angle 0.52497 / 0.29 (13906) SS BOND : bond 0.00198 / 0.12 ( 3) SS BOND : angle 0.30830 / 0.17 ( 6) hydrogen bonds : bond 0.03568 / 2.38 ( 416) hydrogen bonds : angle 5.69714 / 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: 17 poor density : 102 time to evaluate : 0.349 Fit side-chains REVERT: D 86 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: D 148 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.5040 (mmt) REVERT: C 115 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: B 75 MET cc_start: 0.8790 (tpp) cc_final: 0.8058 (ttt) outliers start: 17 outliers final: 7 residues processed: 111 average time/residue: 0.0983 time to fit residues: 15.5213 Evaluate side-chains 107 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN C 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.158213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.123910 restraints weight = 13990.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.128175 restraints weight = 7592.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.130962 restraints weight = 5094.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.132701 restraints weight = 3884.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.133878 restraints weight = 3248.331| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10126 Z= 0.148 Angle : 0.534 5.958 13912 Z= 0.292 Chirality : 0.043 0.144 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.586 82.247 1871 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 16.10 % Favored : 82.15 % 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: 0.13 (0.30), residues: 306 sheet: -1.87 (0.24), residues: 341 loop : -0.62 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 29 TYR 0.014 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 0.00326 / 0.15 (10123) covalent geometry : angle 0.53412 / 0.29 (13906) SS BOND : bond 0.00211 / 0.12 ( 3) SS BOND : angle 0.38075 / 0.20 ( 6) hydrogen bonds : bond 0.03551 / 2.35 ( 416) hydrogen bonds : angle 5.63844 / 3.89 ( 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 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.367 Fit side-chains REVERT: D 86 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: D 148 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.5211 (mmt) REVERT: C 115 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7347 (mt-10) outliers start: 17 outliers final: 9 residues processed: 110 average time/residue: 0.1002 time to fit residues: 15.5926 Evaluate side-chains 112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.157567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123365 restraints weight = 13839.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127616 restraints weight = 7504.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.130365 restraints weight = 5038.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132096 restraints weight = 3846.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133166 restraints weight = 3215.177| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10126 Z= 0.153 Angle : 0.539 6.550 13912 Z= 0.293 Chirality : 0.043 0.150 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.523 81.991 1871 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.65 % Allowed : 16.62 % Favored : 81.73 % 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: -1.23 (0.25), residues: 1107 helix: 0.17 (0.30), residues: 312 sheet: -1.63 (0.25), residues: 351 loop : -0.58 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.005 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10123) covalent geometry : angle 0.53910 / 0.29 (13906) SS BOND : bond 0.00187 / 0.10 ( 3) SS BOND : angle 0.45494 / 0.22 ( 6) hydrogen bonds : bond 0.03502 / 2.28 ( 416) hydrogen bonds : angle 5.63410 / 3.88 ( 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 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.352 Fit side-chains REVERT: D 86 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: D 148 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.5412 (mmt) REVERT: A 196 THR cc_start: 0.7861 (m) cc_final: 0.7600 (p) REVERT: C 115 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7346 (mt-10) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.0985 time to fit residues: 15.4625 Evaluate side-chains 114 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 244 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: 0.4980 chunk 74 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.158634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124733 restraints weight = 13909.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128995 restraints weight = 7507.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.131724 restraints weight = 5016.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.133495 restraints weight = 3823.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134624 restraints weight = 3179.755| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10126 Z= 0.121 Angle : 0.530 8.551 13912 Z= 0.287 Chirality : 0.043 0.164 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.488 81.932 1871 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 17.13 % Favored : 81.42 % 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: -1.15 (0.25), residues: 1107 helix: 0.25 (0.30), residues: 312 sheet: -1.59 (0.25), residues: 350 loop : -0.54 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.013 0.001 TYR D 26 PHE 0.014 0.001 PHE D 207 TRP 0.007 0.001 TRP C 28 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10123) covalent geometry : angle 0.53013 / 0.29 (13906) SS BOND : bond 0.00114 / 0.06 ( 3) SS BOND : angle 0.34560 / 0.19 ( 6) hydrogen bonds : bond 0.03396 / 2.21 ( 416) hydrogen bonds : angle 5.53879 / 3.81 ( 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 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.218 Fit side-chains REVERT: D 86 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.6640 (m-30) REVERT: D 148 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.5366 (mmt) REVERT: C 115 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7247 (mt-10) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 0.0963 time to fit residues: 14.6808 Evaluate side-chains 111 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 MET 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 128 ILE Chi-restraints excluded: chain A residue 235 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 103 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.158817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124821 restraints weight = 13938.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129124 restraints weight = 7529.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.131849 restraints weight = 5020.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133629 restraints weight = 3832.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134775 restraints weight = 3192.255| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10126 Z= 0.122 Angle : 0.529 8.954 13912 Z= 0.286 Chirality : 0.043 0.180 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.447 81.763 1871 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.44 % Allowed : 17.03 % 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: -1.05 (0.25), residues: 1107 helix: 0.32 (0.30), residues: 312 sheet: -1.42 (0.25), residues: 361 loop : -0.55 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.012 0.001 TYR D 26 PHE 0.013 0.001 PHE D 207 TRP 0.007 0.001 TRP C 28 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10123) covalent geometry : angle 0.52924 / 0.29 (13906) SS BOND : bond 0.00136 / 0.08 ( 3) SS BOND : angle 0.27205 / 0.17 ( 6) hydrogen bonds : bond 0.03353 / 2.16 ( 416) hydrogen bonds : angle 5.46271 / 3.76 ( 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 112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.295 Fit side-chains REVERT: D 86 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: D 148 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.5364 (mmt) REVERT: C 115 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7305 (mt-10) outliers start: 14 outliers final: 9 residues processed: 106 average time/residue: 0.0978 time to fit residues: 14.4091 Evaluate side-chains 108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 23 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.0060 chunk 1 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.3946 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.158769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124796 restraints weight = 14037.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129068 restraints weight = 7546.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131789 restraints weight = 5046.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133583 restraints weight = 3862.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134740 restraints weight = 3208.712| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3277 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= 0.119 Angle : 0.534 9.415 13912 Z= 0.285 Chirality : 0.043 0.179 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.420 81.708 1871 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.55 % Allowed : 17.23 % 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: -1.03 (0.25), residues: 1107 helix: 0.34 (0.30), residues: 312 sheet: -1.40 (0.25), residues: 366 loop : -0.53 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.012 0.001 TYR D 26 PHE 0.013 0.001 PHE D 207 TRP 0.007 0.001 TRP C 28 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10123) covalent geometry : angle 0.53365 / 0.29 (13906) SS BOND : bond 0.00127 / 0.07 ( 3) SS BOND : angle 0.30335 / 0.18 ( 6) hydrogen bonds : bond 0.03309 / 2.13 ( 416) hydrogen bonds : angle 5.43311 / 3.73 ( 1142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.37 seconds wall clock time: 29 minutes 52.11 seconds (1792.11 seconds total)