Starting phenix.real_space_refine on Thu Aug 6 08:19:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23bd_68825/08_2026/23bd_68825.cif Found real_map, /net/cci-nas-00/data/ceres_data/23bd_68825/08_2026/23bd_68825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23bd_68825/08_2026/23bd_68825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23bd_68825/08_2026/23bd_68825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23bd_68825/08_2026/23bd_68825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23bd_68825/08_2026/23bd_68825.map" } resolution = 3.4 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 43 5.16 5 C 4431 2.51 5 N 1201 2.21 5 O 1322 1.98 5 H 6959 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13956 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2666 Classifications: {'peptide': 166} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "E" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2924 Classifications: {'peptide': 185} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "C" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1444 Classifications: {'peptide': 88} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "D" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1444 Classifications: {'peptide': 88} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "A" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5478 Classifications: {'peptide': 351} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 330} Chain breaks: 3 Time building chain proxies: 2.58, per 1000 atoms: 0.18 Number of scatterers: 13956 At special positions: 0 Unit cell: (123.25, 85, 98.6, 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 43 16.00 O 1322 8.00 N 1201 7.00 C 4431 6.00 H 6959 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.27 Conformation dependent library (CDL) restraints added in 460.0 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 41.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 154 through 169 removed outlier: 3.908A pdb=" N ASP B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.773A pdb=" N HIS B 197 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 198 " --> pdb=" O PRO B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 198' Processing helix chain 'B' and resid 231 through 238 Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.656A pdb=" N LEU B 246 " --> pdb=" O CYS B 243 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 247 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 247' Processing helix chain 'E' and resid 110 through 121 removed outlier: 3.632A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 removed outlier: 3.601A pdb=" N ARG E 134 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.686A pdb=" N ASP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 164 " --> pdb=" O THR E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.592A pdb=" N HIS E 197 " --> pdb=" O ARG E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 239 removed outlier: 3.654A pdb=" N PHE E 235 " --> pdb=" O TYR E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 removed outlier: 3.678A pdb=" N GLN E 281 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 338 through 350 removed outlier: 3.626A pdb=" N PHE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 334 Processing helix chain 'D' and resid 338 through 350 removed outlier: 3.649A pdb=" N PHE D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.576A pdb=" N VAL A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 13 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 126 through 137 removed outlier: 4.277A pdb=" N TRP A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS A 135 " --> pdb=" O GLN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 286 through 302 Processing helix chain 'A' and resid 305 through 321 removed outlier: 4.030A pdb=" N LEU A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.539A pdb=" N ALA A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 382 through 396 removed outlier: 3.710A pdb=" N HIS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.642A pdb=" N GLU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.726A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.573A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 480 Processing sheet with id=AA1, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.644A pdb=" N PHE B 204 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR B 203 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 254 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B 205 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLN B 256 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 207 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS B 251 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE C 303 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE B 253 " --> pdb=" O PHE C 303 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 215 through 217 Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.635A pdb=" N THR D 294 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.472A pdb=" N LYS E 251 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE D 303 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE E 253 " --> pdb=" O PHE D 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 211 through 212 removed outlier: 3.636A pdb=" N GLY E 215 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 265 through 269 Processing sheet with id=AA7, first strand: chain 'E' and resid 286 through 288 Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 42 removed outlier: 3.729A pdb=" N ASN A 156 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 39 through 42 removed outlier: 3.729A pdb=" N ASN A 156 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N ASN A 156 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N ILE A 223 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR A 158 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 221 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL A 160 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 219 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 215 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR A 166 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR A 213 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 420 through 421 removed outlier: 4.081A pdb=" N GLU A 448 " --> pdb=" O CYS A 457 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6934 1.03 - 1.23: 31 1.23 - 1.42: 2946 1.42 - 1.62: 4126 1.62 - 1.81: 61 Bond restraints: 14098 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N MET A 1 " pdb=" H MET A 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" N GLU E 177 " pdb=" CA GLU E 177 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.79e+00 bond pdb=" N PRO E 150 " pdb=" CA PRO E 150 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.31e-02 5.83e+03 1.08e+00 bond pdb=" CB GLU A 317 " pdb=" CG GLU A 317 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.08e-01 ... (remaining 14093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 23447 1.04 - 2.08: 1869 2.08 - 3.12: 121 3.12 - 4.16: 52 4.16 - 5.20: 16 Bond angle restraints: 25505 Sorted by residual: angle pdb=" C GLU E 177 " pdb=" CA GLU E 177 " pdb=" CB GLU E 177 " ideal model delta sigma weight residual 110.42 115.40 -4.98 1.99e+00 2.53e-01 6.27e+00 angle pdb=" C HIS E 210 " pdb=" N GLY E 211 " pdb=" CA GLY E 211 " ideal model delta sigma weight residual 120.86 117.00 3.86 1.62e+00 3.81e-01 5.69e+00 angle pdb=" CA GLU A 383 " pdb=" CB GLU A 383 " pdb=" CG GLU A 383 " ideal model delta sigma weight residual 114.10 118.81 -4.71 2.00e+00 2.50e-01 5.55e+00 angle pdb=" CA GLU A 317 " pdb=" CB GLU A 317 " pdb=" CG GLU A 317 " ideal model delta sigma weight residual 114.10 118.71 -4.61 2.00e+00 2.50e-01 5.30e+00 angle pdb=" N GLY E 211 " pdb=" CA GLY E 211 " pdb=" C GLY E 211 " ideal model delta sigma weight residual 110.42 113.79 -3.37 1.49e+00 4.50e-01 5.12e+00 ... (remaining 25500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 5737 16.72 - 33.43: 599 33.43 - 50.15: 186 50.15 - 66.86: 69 66.86 - 83.58: 25 Dihedral angle restraints: 6616 sinusoidal: 3641 harmonic: 2975 Sorted by residual: dihedral pdb=" CA ILE E 216 " pdb=" C ILE E 216 " pdb=" N CYS E 217 " pdb=" CA CYS E 217 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA SER E 209 " pdb=" C SER E 209 " pdb=" N HIS E 210 " pdb=" CA HIS E 210 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LYS A 43 " pdb=" C LYS A 43 " pdb=" N PRO A 44 " pdb=" CA PRO A 44 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 6613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 668 0.029 - 0.058: 302 0.058 - 0.087: 56 0.087 - 0.117: 45 0.117 - 0.146: 16 Chirality restraints: 1087 Sorted by residual: chirality pdb=" CA ILE A 23 " pdb=" N ILE A 23 " pdb=" C ILE A 23 " pdb=" CB ILE A 23 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA VAL A 364 " pdb=" N VAL A 364 " pdb=" C VAL A 364 " pdb=" CB VAL A 364 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE E 254 " pdb=" N ILE E 254 " pdb=" C ILE E 254 " pdb=" CB ILE E 254 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1084 not shown) Planarity restraints: 2078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 241 " -0.183 9.50e-02 1.11e+02 6.12e-02 4.48e+00 pdb=" NE ARG E 241 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG E 241 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 241 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 241 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 241 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG E 241 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG E 241 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 241 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 317 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" CD GLU A 317 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU A 317 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 317 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 307 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO D 308 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 308 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 308 " -0.027 5.00e-02 4.00e+02 ... (remaining 2075 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.48: 9456 2.48 - 3.01: 31783 3.01 - 3.54: 36408 3.54 - 4.07: 48187 4.07 - 4.60: 70761 Nonbonded interactions: 196595 Sorted by model distance: nonbonded pdb=" H SER A 225 " pdb=" H ASP A 226 " model vdw 1.950 2.100 nonbonded pdb=" H LEU A 214 " pdb=" H ALA A 215 " model vdw 1.968 2.100 nonbonded pdb=" HE ARG B 131 " pdb="HH22 ARG B 134 " model vdw 1.973 2.100 nonbonded pdb=" H THR C 317 " pdb=" H MET C 318 " model vdw 1.979 2.100 nonbonded pdb=" H VAL A 157 " pdb=" HG1 THR A 239 " model vdw 1.984 2.100 ... (remaining 196590 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 'B' selection = (chain 'E' and resid 105 through 270) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.003 0.032 7139 Z= 0.134 Angle : 0.566 5.200 9665 Z= 0.291 Chirality : 0.039 0.146 1087 Planarity : 0.004 0.080 1251 Dihedral : 16.447 83.575 2677 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.64 % Allowed : 13.97 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 (0.28), residues: 862 helix: 0.19 (0.30), residues: 306 sheet: -2.35 (0.51), residues: 92 loop : -0.89 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 241 TYR 0.007 0.001 TYR C 292 PHE 0.010 0.001 PHE C 303 TRP 0.007 0.001 TRP C 313 HIS 0.003 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 7139) covalent geometry : angle 0.56578 / 0.29 ( 9665) hydrogen bonds : bond 0.21657 / 14.13 ( 265) hydrogen bonds : angle 8.61716 / 6.11 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.4203 (pmm) cc_final: 0.1372 (ttm) REVERT: A 297 ILE cc_start: 0.8598 (pt) cc_final: 0.8335 (mt) outliers start: 5 outliers final: 4 residues processed: 82 average time/residue: 0.2427 time to fit residues: 25.1245 Evaluate side-chains 59 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0020 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046893 restraints weight = 77607.854| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.69 r_work: 0.2842 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7139 Z= 0.237 Angle : 0.550 4.670 9665 Z= 0.296 Chirality : 0.039 0.135 1087 Planarity : 0.004 0.046 1251 Dihedral : 5.136 54.557 954 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.54 % Allowed : 15.00 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.29), residues: 862 helix: 0.84 (0.29), residues: 318 sheet: -1.95 (0.56), residues: 94 loop : -0.92 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 344 TYR 0.016 0.002 TYR A 373 PHE 0.007 0.001 PHE A 5 TRP 0.012 0.001 TRP A 130 HIS 0.005 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 ( 7139) covalent geometry : angle 0.55002 / 0.30 ( 9665) hydrogen bonds : bond 0.04499 / 2.80 ( 265) hydrogen bonds : angle 6.04407 / 4.41 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1557 (tmm) cc_final: 0.0971 (tpt) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.2030 time to fit residues: 18.1883 Evaluate side-chains 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.064300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047296 restraints weight = 77279.753| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.70 r_work: 0.2859 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7139 Z= 0.120 Angle : 0.467 4.562 9665 Z= 0.244 Chirality : 0.038 0.140 1087 Planarity : 0.003 0.040 1251 Dihedral : 4.512 37.845 951 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.28 % Allowed : 14.36 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.29), residues: 862 helix: 1.19 (0.30), residues: 317 sheet: -1.75 (0.59), residues: 92 loop : -0.82 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 344 TYR 0.010 0.001 TYR A 158 PHE 0.007 0.001 PHE A 216 TRP 0.006 0.001 TRP A 439 HIS 0.008 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 7139) covalent geometry : angle 0.46656 / 0.24 ( 9665) hydrogen bonds : bond 0.03478 / 2.16 ( 265) hydrogen bonds : angle 5.38133 / 3.94 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 59 average time/residue: 0.2140 time to fit residues: 16.3868 Evaluate side-chains 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 133 ASN A 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046868 restraints weight = 77076.390| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.65 r_work: 0.2854 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7139 Z= 0.144 Angle : 0.464 4.671 9665 Z= 0.241 Chirality : 0.037 0.136 1087 Planarity : 0.003 0.037 1251 Dihedral : 4.425 37.771 951 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.28 % Allowed : 14.49 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.30), residues: 862 helix: 1.34 (0.30), residues: 318 sheet: -1.74 (0.58), residues: 94 loop : -0.74 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 344 TYR 0.008 0.001 TYR A 470 PHE 0.006 0.001 PHE A 216 TRP 0.006 0.001 TRP C 313 HIS 0.003 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7139) covalent geometry : angle 0.46426 / 0.24 ( 9665) hydrogen bonds : bond 0.02882 / 1.77 ( 265) hydrogen bonds : angle 4.98853 / 3.68 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1576 (tmm) cc_final: 0.0966 (tpt) REVERT: A 362 MET cc_start: 0.8875 (mtp) cc_final: 0.8412 (mmm) outliers start: 10 outliers final: 9 residues processed: 58 average time/residue: 0.2128 time to fit residues: 16.1487 Evaluate side-chains 57 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.063949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046928 restraints weight = 77506.994| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.69 r_work: 0.2852 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7139 Z= 0.131 Angle : 0.461 5.777 9665 Z= 0.238 Chirality : 0.037 0.138 1087 Planarity : 0.003 0.035 1251 Dihedral : 4.389 37.692 951 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.67 % Allowed : 14.10 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.30), residues: 862 helix: 1.48 (0.30), residues: 318 sheet: -1.81 (0.58), residues: 94 loop : -0.74 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 259 TYR 0.007 0.001 TYR A 470 PHE 0.007 0.001 PHE A 216 TRP 0.006 0.001 TRP C 313 HIS 0.003 0.000 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7139) covalent geometry : angle 0.46100 / 0.24 ( 9665) hydrogen bonds : bond 0.02773 / 1.70 ( 265) hydrogen bonds : angle 4.86694 / 3.58 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1477 (tmm) cc_final: 0.0878 (tpt) REVERT: A 299 LYS cc_start: 0.9476 (mmmm) cc_final: 0.9148 (tptt) REVERT: A 362 MET cc_start: 0.8879 (mtp) cc_final: 0.8405 (mmm) outliers start: 13 outliers final: 11 residues processed: 59 average time/residue: 0.2074 time to fit residues: 16.1212 Evaluate side-chains 59 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.064589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.047567 restraints weight = 76817.053| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.70 r_work: 0.2870 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7139 Z= 0.090 Angle : 0.439 4.396 9665 Z= 0.225 Chirality : 0.037 0.136 1087 Planarity : 0.003 0.031 1251 Dihedral : 4.241 36.758 951 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.28 % Allowed : 14.49 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.30), residues: 862 helix: 1.73 (0.30), residues: 318 sheet: -1.78 (0.59), residues: 92 loop : -0.61 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 259 TYR 0.006 0.001 TYR C 292 PHE 0.007 0.001 PHE A 216 TRP 0.006 0.001 TRP C 313 HIS 0.003 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 7139) covalent geometry : angle 0.43937 / 0.23 ( 9665) hydrogen bonds : bond 0.02564 / 1.57 ( 265) hydrogen bonds : angle 4.65870 / 3.44 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 236 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 1 MET cc_start: 0.1342 (tmm) cc_final: 0.0801 (tpt) REVERT: A 299 LYS cc_start: 0.9480 (mmmm) cc_final: 0.9266 (mmmt) REVERT: A 362 MET cc_start: 0.8888 (mtp) cc_final: 0.8411 (mmm) REVERT: A 466 MET cc_start: 0.8885 (mmm) cc_final: 0.8624 (mmm) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.2003 time to fit residues: 14.8295 Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.063474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046485 restraints weight = 76969.661| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.66 r_work: 0.2839 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7139 Z= 0.159 Angle : 0.469 5.234 9665 Z= 0.241 Chirality : 0.037 0.133 1087 Planarity : 0.003 0.033 1251 Dihedral : 4.328 37.635 951 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.28 % Allowed : 14.62 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.30), residues: 862 helix: 1.74 (0.30), residues: 318 sheet: -1.77 (0.59), residues: 92 loop : -0.67 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 259 TYR 0.008 0.001 TYR A 54 PHE 0.008 0.001 PHE A 287 TRP 0.006 0.001 TRP A 439 HIS 0.004 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 7139) covalent geometry : angle 0.46930 / 0.24 ( 9665) hydrogen bonds : bond 0.02677 / 1.64 ( 265) hydrogen bonds : angle 4.67118 / 3.46 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 236 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 1 MET cc_start: 0.1574 (tmm) cc_final: 0.1030 (tpt) REVERT: A 299 LYS cc_start: 0.9490 (mmmm) cc_final: 0.9255 (mmmt) REVERT: A 362 MET cc_start: 0.8891 (mtp) cc_final: 0.8429 (mmm) REVERT: A 466 MET cc_start: 0.8907 (mmm) cc_final: 0.8640 (mmm) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.1930 time to fit residues: 14.5768 Evaluate side-chains 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.062720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045714 restraints weight = 77533.051| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.61 r_work: 0.2820 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7139 Z= 0.198 Angle : 0.492 6.538 9665 Z= 0.256 Chirality : 0.038 0.136 1087 Planarity : 0.003 0.033 1251 Dihedral : 4.455 37.915 951 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.28 % Allowed : 14.74 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.30), residues: 862 helix: 1.65 (0.30), residues: 319 sheet: -1.63 (0.59), residues: 90 loop : -0.80 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 259 TYR 0.011 0.001 TYR A 54 PHE 0.009 0.001 PHE B 235 TRP 0.009 0.001 TRP A 439 HIS 0.004 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 7139) covalent geometry : angle 0.49197 / 0.26 ( 9665) hydrogen bonds : bond 0.02784 / 1.71 ( 265) hydrogen bonds : angle 4.70919 / 3.50 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 363 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8176 (mp0) REVERT: A 1 MET cc_start: 0.1785 (tmm) cc_final: 0.1228 (tpt) REVERT: A 299 LYS cc_start: 0.9501 (mmmm) cc_final: 0.9152 (tptt) REVERT: A 362 MET cc_start: 0.8882 (mtp) cc_final: 0.8433 (mmm) REVERT: A 466 MET cc_start: 0.8917 (mmm) cc_final: 0.8654 (mmm) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.1851 time to fit residues: 13.9832 Evaluate side-chains 57 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.063787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046763 restraints weight = 77255.910| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.66 r_work: 0.2854 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7139 Z= 0.094 Angle : 0.449 5.116 9665 Z= 0.229 Chirality : 0.038 0.138 1087 Planarity : 0.003 0.032 1251 Dihedral : 4.277 36.633 951 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.90 % Allowed : 15.51 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.30), residues: 862 helix: 1.93 (0.30), residues: 319 sheet: -1.64 (0.59), residues: 90 loop : -0.65 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 344 TYR 0.006 0.001 TYR C 292 PHE 0.008 0.001 PHE A 216 TRP 0.007 0.001 TRP C 313 HIS 0.003 0.000 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 ( 7139) covalent geometry : angle 0.44872 / 0.23 ( 9665) hydrogen bonds : bond 0.02446 / 1.51 ( 265) hydrogen bonds : angle 4.48833 / 3.34 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 236 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7835 (tm-30) REVERT: C 363 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8159 (mp0) REVERT: A 1 MET cc_start: 0.1672 (tmm) cc_final: 0.1137 (tpt) REVERT: A 299 LYS cc_start: 0.9498 (mmmm) cc_final: 0.9236 (mmmt) REVERT: A 466 MET cc_start: 0.8881 (mmm) cc_final: 0.8626 (mmm) outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.1783 time to fit residues: 12.8808 Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.064050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047041 restraints weight = 76905.551| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.67 r_work: 0.2861 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7139 Z= 0.096 Angle : 0.443 6.485 9665 Z= 0.225 Chirality : 0.037 0.137 1087 Planarity : 0.003 0.032 1251 Dihedral : 4.164 36.475 951 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.03 % Allowed : 15.26 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.30), residues: 862 helix: 2.06 (0.30), residues: 320 sheet: -1.59 (0.59), residues: 90 loop : -0.55 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 344 TYR 0.005 0.001 TYR A 54 PHE 0.006 0.001 PHE A 216 TRP 0.007 0.001 TRP C 313 HIS 0.004 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 7139) covalent geometry : angle 0.44288 / 0.22 ( 9665) hydrogen bonds : bond 0.02341 / 1.45 ( 265) hydrogen bonds : angle 4.36775 / 3.25 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 236 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 363 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8153 (mp0) REVERT: A 1 MET cc_start: 0.1563 (tmm) cc_final: 0.1057 (tpt) REVERT: A 299 LYS cc_start: 0.9502 (mmmm) cc_final: 0.9245 (mmmt) REVERT: A 466 MET cc_start: 0.8870 (mmm) cc_final: 0.8628 (mmm) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.1931 time to fit residues: 14.5078 Evaluate side-chains 57 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 chunk 1 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.064300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047280 restraints weight = 76915.515| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.69 r_work: 0.2868 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7139 Z= 0.086 Angle : 0.438 5.819 9665 Z= 0.222 Chirality : 0.037 0.136 1087 Planarity : 0.003 0.033 1251 Dihedral : 4.109 36.258 951 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.03 % Allowed : 15.26 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.30), residues: 862 helix: 2.17 (0.30), residues: 321 sheet: -1.57 (0.58), residues: 90 loop : -0.52 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 344 TYR 0.005 0.001 TYR A 54 PHE 0.007 0.001 PHE A 216 TRP 0.006 0.001 TRP C 313 HIS 0.004 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 7139) covalent geometry : angle 0.43819 / 0.22 ( 9665) hydrogen bonds : bond 0.02287 / 1.41 ( 265) hydrogen bonds : angle 4.29947 / 3.20 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.96 seconds wall clock time: 45 minutes 59.56 seconds (2759.56 seconds total)