Starting phenix.real_space_refine on Wed Sep 17 07:22:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6v_50241/09_2025/9f6v_50241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6v_50241/09_2025/9f6v_50241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f6v_50241/09_2025/9f6v_50241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6v_50241/09_2025/9f6v_50241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f6v_50241/09_2025/9f6v_50241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6v_50241/09_2025/9f6v_50241.map" } resolution = 3.5 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= -0.004 sd= 0.172 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 P 3 5.49 5 S 34 5.16 5 C 4206 2.51 5 N 1093 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6610 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3230 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406} Chain: "D" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3348 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 405} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.27 Number of scatterers: 6610 At special positions: 0 Unit cell: (98.8, 75.4, 104, 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 34 16.00 P 3 15.00 O 1274 8.00 N 1093 7.00 C 4206 6.00 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: 0.64 Conformation dependent library (CDL) restraints added in 394.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 52.1% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 11 through 29 Processing helix chain 'A' and resid 44 through 47 Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.622A pdb=" N VAL A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 138 through 155 removed outlier: 3.715A pdb=" N GLY A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 192 removed outlier: 3.603A pdb=" N ASN A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 318 through 333 Processing helix chain 'A' and resid 368 through 384 removed outlier: 4.271A pdb=" N PHE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 removed outlier: 3.822A pdb=" N PHE A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 420 Processing helix chain 'D' and resid 11 through 29 Proline residue: D 19 - end of helix Processing helix chain 'D' and resid 44 through 47 Processing helix chain 'D' and resid 68 through 77 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 98 through 104 removed outlier: 3.999A pdb=" N GLY D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 Processing helix chain 'D' and resid 110 through 123 Processing helix chain 'D' and resid 139 through 155 Proline residue: D 147 - end of helix Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.869A pdb=" N LYS D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 219 through 237 removed outlier: 4.296A pdb=" N THR D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 320 through 328 Processing helix chain 'D' and resid 329 through 332 Processing helix chain 'D' and resid 369 through 386 removed outlier: 3.774A pdb=" N LEU D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 401 through 421 removed outlier: 3.700A pdb=" N ASP D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 8.345A pdb=" N VAL A 87 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 62 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU A 4 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 129 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 6 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU A 131 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 8 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS A 133 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 10 " --> pdb=" O HIS A 133 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE A 161 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 129 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE A 163 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 131 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE A 165 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS A 133 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 160 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A 196 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 162 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A 198 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER A 164 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER A 195 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA A 264 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 197 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N THR A 266 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 13.038A pdb=" N ASP A 199 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE A 261 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN A 365 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 308 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA3, first strand: chain 'D' and resid 88 through 90 removed outlier: 8.178A pdb=" N VAL D 89 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU D 63 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N ILE D 62 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR D 7 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL D 64 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS D 9 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU D 4 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N PHE D 131 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE D 6 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL D 133 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 8 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS D 135 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL D 10 " --> pdb=" O HIS D 135 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN D 129 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N MET D 163 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE D 131 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TYR D 165 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL D 133 " --> pdb=" O TYR D 165 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE D 167 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N HIS D 135 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER D 197 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR D 266 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE D 199 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N MET D 268 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N ASP D 201 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N PHE D 263 " --> pdb=" O HIS D 367 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N HIS D 367 " --> pdb=" O PHE D 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.318A pdb=" N GLN D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 49 through 51 325 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2128 1.33 - 1.45: 1293 1.45 - 1.57: 3255 1.57 - 1.69: 5 1.69 - 1.81: 58 Bond restraints: 6739 Sorted by residual: bond pdb=" CB ASN A 364 " pdb=" CG ASN A 364 " ideal model delta sigma weight residual 1.516 1.338 0.178 2.50e-02 1.60e+03 5.08e+01 bond pdb=" CB TRP A 338 " pdb=" CG TRP A 338 " ideal model delta sigma weight residual 1.498 1.290 0.208 3.10e-02 1.04e+03 4.50e+01 bond pdb=" CA TRP A 391 " pdb=" C TRP A 391 " ideal model delta sigma weight residual 1.524 1.463 0.062 1.24e-02 6.50e+03 2.46e+01 bond pdb=" CG TRP A 338 " pdb=" CD2 TRP A 338 " ideal model delta sigma weight residual 1.433 1.345 0.088 1.80e-02 3.09e+03 2.37e+01 bond pdb=" CA TRP A 338 " pdb=" C TRP A 338 " ideal model delta sigma weight residual 1.522 1.457 0.066 1.36e-02 5.41e+03 2.34e+01 ... (remaining 6734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 8466 2.76 - 5.52: 593 5.52 - 8.28: 53 8.28 - 11.04: 7 11.04 - 13.80: 4 Bond angle restraints: 9123 Sorted by residual: angle pdb=" N TRP A 391 " pdb=" CA TRP A 391 " pdb=" C TRP A 391 " ideal model delta sigma weight residual 110.97 103.74 7.23 1.09e+00 8.42e-01 4.40e+01 angle pdb=" C SER A 239 " pdb=" CA SER A 239 " pdb=" CB SER A 239 " ideal model delta sigma weight residual 116.63 109.07 7.56 1.16e+00 7.43e-01 4.25e+01 angle pdb=" C ALA D 183 " pdb=" N ILE D 184 " pdb=" CA ILE D 184 " ideal model delta sigma weight residual 121.02 111.65 9.37 1.51e+00 4.39e-01 3.85e+01 angle pdb=" C ASP A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta sigma weight residual 119.56 125.26 -5.70 1.02e+00 9.61e-01 3.12e+01 angle pdb=" C THR D 61 " pdb=" CA THR D 61 " pdb=" CB THR D 61 " ideal model delta sigma weight residual 109.79 98.35 11.44 2.05e+00 2.38e-01 3.11e+01 ... (remaining 9118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 4006 35.92 - 71.84: 43 71.84 - 107.76: 3 107.76 - 143.68: 3 143.68 - 179.61: 2 Dihedral angle restraints: 4057 sinusoidal: 1620 harmonic: 2437 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -110.34 179.61 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -65.14 169.74 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2G GTP A 501 " pdb=" O3B GTP A 501 " pdb=" PG GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 177.30 -45.92 -136.78 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 4054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 540 0.068 - 0.137: 346 0.137 - 0.205: 128 0.205 - 0.274: 22 0.274 - 0.342: 3 Chirality restraints: 1039 Sorted by residual: chirality pdb=" CB ILE D 184 " pdb=" CA ILE D 184 " pdb=" CG1 ILE D 184 " pdb=" CG2 ILE D 184 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CG LEU D 179 " pdb=" CB LEU D 179 " pdb=" CD1 LEU D 179 " pdb=" CD2 LEU D 179 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1036 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 22 " -0.043 2.00e-02 2.50e+03 2.13e-02 1.14e+01 pdb=" CG TRP D 22 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP D 22 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 22 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP D 22 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP D 22 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP D 22 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 22 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 22 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 22 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 61 " -0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C THR D 61 " 0.058 2.00e-02 2.50e+03 pdb=" O THR D 61 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE D 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 338 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.65e+00 pdb=" C TRP A 338 " -0.054 2.00e-02 2.50e+03 pdb=" O TRP A 338 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE A 339 " 0.018 2.00e-02 2.50e+03 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2119 2.81 - 3.34: 6518 3.34 - 3.86: 11061 3.86 - 4.38: 13731 4.38 - 4.90: 22092 Nonbonded interactions: 55521 Sorted by model distance: nonbonded pdb=" N VAL A 176 " pdb=" N GLU A 177 " model vdw 2.292 2.560 nonbonded pdb=" OD1 ASN A 200 " pdb=" N2 GTP A 501 " model vdw 2.384 3.120 nonbonded pdb=" N ASP D 95 " pdb=" OD1 ASP D 95 " model vdw 2.413 3.120 nonbonded pdb=" N ASP D 174 " pdb=" OD1 ASP D 174 " model vdw 2.434 3.120 nonbonded pdb=" OD2 ASP D 84 " pdb=" NZ LYS D 86 " model vdw 2.445 3.120 ... (remaining 55516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.110 Find NCS groups from input model: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 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 : 0.023 0.208 6739 Z= 1.207 Angle : 1.549 13.804 9123 Z= 0.979 Chirality : 0.095 0.342 1039 Planarity : 0.008 0.049 1168 Dihedral : 12.465 179.606 2483 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.30 (0.28), residues: 840 helix: 0.14 (0.25), residues: 358 sheet: 1.56 (0.46), residues: 123 loop : -0.08 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 59 TYR 0.031 0.006 TYR D 394 PHE 0.042 0.006 PHE A 313 TRP 0.043 0.007 TRP D 22 HIS 0.010 0.003 HIS D 321 Details of bonding type rmsd covalent geometry : bond 0.02345 ( 6739) covalent geometry : angle 1.54918 ( 9123) hydrogen bonds : bond 0.17422 ( 325) hydrogen bonds : angle 6.92545 ( 930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.188 Fit side-chains REVERT: A 63 VAL cc_start: 0.7673 (t) cc_final: 0.7265 (p) REVERT: A 209 LYS cc_start: 0.7361 (mmtt) cc_final: 0.7095 (mtmt) REVERT: D 36 GLN cc_start: 0.7638 (tp40) cc_final: 0.7350 (mm-40) REVERT: D 76 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7970 (mtmt) REVERT: D 81 ASP cc_start: 0.6980 (m-30) cc_final: 0.6530 (t0) REVERT: D 123 ASP cc_start: 0.7106 (m-30) cc_final: 0.6728 (m-30) REVERT: D 127 HIS cc_start: 0.6772 (m-70) cc_final: 0.6439 (m170) REVERT: D 198 MET cc_start: 0.7158 (mtt) cc_final: 0.6705 (ttm) REVERT: D 249 MET cc_start: 0.6840 (tpp) cc_final: 0.6521 (tpp) REVERT: D 268 MET cc_start: 0.8358 (mtp) cc_final: 0.7826 (ttp) REVERT: D 403 GLU cc_start: 0.6689 (tp30) cc_final: 0.6291 (tp30) REVERT: D 410 ASN cc_start: 0.6799 (m-40) cc_final: 0.6511 (t0) REVERT: D 417 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6971 (mt-10) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1112 time to fit residues: 25.6007 Evaluate side-chains 104 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 12 GLN ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN D 171 GLN D 216 ASN D 279 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.189056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159474 restraints weight = 7112.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.163690 restraints weight = 4558.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.166561 restraints weight = 3369.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168184 restraints weight = 2745.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169600 restraints weight = 2410.634| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6739 Z= 0.189 Angle : 0.657 7.225 9123 Z= 0.359 Chirality : 0.049 0.182 1039 Planarity : 0.005 0.055 1168 Dihedral : 12.299 164.802 904 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.21 % Allowed : 6.50 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.71 (0.29), residues: 840 helix: 1.04 (0.27), residues: 361 sheet: 1.23 (0.46), residues: 136 loop : -0.38 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 239 TYR 0.012 0.002 TYR A 306 PHE 0.026 0.002 PHE A 97 TRP 0.020 0.002 TRP D 22 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 6739) covalent geometry : angle 0.65700 ( 9123) hydrogen bonds : bond 0.05107 ( 325) hydrogen bonds : angle 4.96946 ( 930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.231 Fit side-chains REVERT: A 46 ASP cc_start: 0.7397 (t70) cc_final: 0.7193 (t0) REVERT: A 222 ASN cc_start: 0.8110 (m-40) cc_final: 0.7219 (m-40) REVERT: A 367 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7759 (mm-30) outliers start: 16 outliers final: 6 residues processed: 132 average time/residue: 0.0882 time to fit residues: 15.4942 Evaluate side-chains 93 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS D 16 GLN D 36 GLN ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.182004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.152128 restraints weight = 7076.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156092 restraints weight = 4606.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158815 restraints weight = 3455.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.160480 restraints weight = 2845.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161716 restraints weight = 2503.182| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6739 Z= 0.189 Angle : 0.597 5.939 9123 Z= 0.324 Chirality : 0.048 0.166 1039 Planarity : 0.004 0.051 1168 Dihedral : 11.760 161.609 904 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.21 % Allowed : 9.41 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.62 (0.29), residues: 840 helix: 1.24 (0.27), residues: 368 sheet: 0.70 (0.46), residues: 144 loop : -0.63 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 381 TYR 0.013 0.001 TYR A 306 PHE 0.018 0.002 PHE D 381 TRP 0.018 0.002 TRP D 22 HIS 0.003 0.001 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 6739) covalent geometry : angle 0.59745 ( 9123) hydrogen bonds : bond 0.04756 ( 325) hydrogen bonds : angle 4.62319 ( 930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.259 Fit side-chains REVERT: A 222 ASN cc_start: 0.8133 (m-40) cc_final: 0.7257 (m-40) REVERT: A 367 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7861 (mm-30) REVERT: D 65 ASP cc_start: 0.7139 (t0) cc_final: 0.6877 (t0) REVERT: D 304 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7651 (tm-30) REVERT: D 394 TYR cc_start: 0.9020 (m-80) cc_final: 0.8779 (m-80) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.0870 time to fit residues: 12.9036 Evaluate side-chains 92 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 418 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 0.0050 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 19 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.195197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164966 restraints weight = 7118.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168957 restraints weight = 4710.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.171840 restraints weight = 3565.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.173406 restraints weight = 2937.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.174905 restraints weight = 2602.184| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6739 Z= 0.113 Angle : 0.515 6.379 9123 Z= 0.277 Chirality : 0.045 0.162 1039 Planarity : 0.004 0.040 1168 Dihedral : 11.428 158.600 904 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.49 % Allowed : 11.07 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.75 (0.29), residues: 840 helix: 1.47 (0.27), residues: 383 sheet: 0.78 (0.46), residues: 135 loop : -0.79 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 239 TYR 0.019 0.001 TYR A 191 PHE 0.013 0.001 PHE A 313 TRP 0.015 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6739) covalent geometry : angle 0.51499 ( 9123) hydrogen bonds : bond 0.03805 ( 325) hydrogen bonds : angle 4.38583 ( 930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.257 Fit side-chains REVERT: A 123 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7529 (m) REVERT: A 222 ASN cc_start: 0.7943 (m-40) cc_final: 0.7345 (m-40) REVERT: A 239 SER cc_start: 0.9168 (t) cc_final: 0.8961 (p) REVERT: A 305 ARG cc_start: 0.8650 (mtp-110) cc_final: 0.8267 (mtp85) REVERT: A 365 ASN cc_start: 0.7576 (t0) cc_final: 0.7301 (t0) REVERT: A 416 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.6290 (t80) REVERT: D 65 ASP cc_start: 0.7101 (t0) cc_final: 0.6810 (t0) REVERT: D 123 ASP cc_start: 0.6809 (t0) cc_final: 0.6588 (m-30) REVERT: D 163 MET cc_start: 0.7210 (ttt) cc_final: 0.6822 (ttt) REVERT: D 394 TYR cc_start: 0.8858 (m-80) cc_final: 0.8500 (m-80) REVERT: D 418 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.6093 (t80) outliers start: 18 outliers final: 6 residues processed: 118 average time/residue: 0.0864 time to fit residues: 13.6488 Evaluate side-chains 100 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 418 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 3 optimal weight: 0.0030 chunk 67 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.192518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162122 restraints weight = 7120.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166284 restraints weight = 4691.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169048 restraints weight = 3536.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170998 restraints weight = 2916.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171997 restraints weight = 2565.106| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6739 Z= 0.122 Angle : 0.512 6.484 9123 Z= 0.272 Chirality : 0.045 0.154 1039 Planarity : 0.003 0.037 1168 Dihedral : 11.211 155.789 904 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.49 % Allowed : 12.31 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.78 (0.29), residues: 840 helix: 1.61 (0.27), residues: 385 sheet: 0.63 (0.45), residues: 135 loop : -0.86 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 239 TYR 0.013 0.001 TYR A 191 PHE 0.014 0.001 PHE D 381 TRP 0.015 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6739) covalent geometry : angle 0.51189 ( 9123) hydrogen bonds : bond 0.03796 ( 325) hydrogen bonds : angle 4.24325 ( 930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.271 Fit side-chains REVERT: A 123 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7517 (m) REVERT: A 222 ASN cc_start: 0.7950 (m-40) cc_final: 0.7429 (m-40) REVERT: A 293 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6488 (mt-10) REVERT: A 305 ARG cc_start: 0.8512 (mtp-110) cc_final: 0.8191 (mtp85) REVERT: A 365 ASN cc_start: 0.7617 (t0) cc_final: 0.7410 (t0) REVERT: A 416 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6228 (t80) REVERT: D 65 ASP cc_start: 0.7064 (t0) cc_final: 0.6720 (t0) REVERT: D 304 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 394 TYR cc_start: 0.8847 (m-80) cc_final: 0.8383 (m-80) REVERT: D 417 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7099 (mt-10) outliers start: 18 outliers final: 7 residues processed: 112 average time/residue: 0.0911 time to fit residues: 13.7152 Evaluate side-chains 108 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.188485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157803 restraints weight = 7125.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.161771 restraints weight = 4743.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164570 restraints weight = 3603.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.166121 restraints weight = 2990.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167535 restraints weight = 2654.929| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6739 Z= 0.150 Angle : 0.545 7.555 9123 Z= 0.286 Chirality : 0.046 0.159 1039 Planarity : 0.004 0.038 1168 Dihedral : 11.129 154.456 904 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.49 % Allowed : 13.83 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.70 (0.29), residues: 840 helix: 1.66 (0.27), residues: 380 sheet: 0.42 (0.44), residues: 135 loop : -0.96 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 239 TYR 0.015 0.001 TYR D 395 PHE 0.021 0.002 PHE A 97 TRP 0.014 0.002 TRP D 22 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6739) covalent geometry : angle 0.54541 ( 9123) hydrogen bonds : bond 0.03997 ( 325) hydrogen bonds : angle 4.21886 ( 930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.246 Fit side-chains REVERT: A 107 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6542 (mm-30) REVERT: A 123 THR cc_start: 0.7965 (m) cc_final: 0.7613 (m) REVERT: A 222 ASN cc_start: 0.8039 (m-40) cc_final: 0.7478 (m-40) REVERT: A 293 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6584 (mt-10) REVERT: A 305 ARG cc_start: 0.8542 (mtp-110) cc_final: 0.8260 (mtp85) REVERT: A 365 ASN cc_start: 0.7690 (t0) cc_final: 0.7394 (t0) REVERT: A 416 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6061 (t80) REVERT: D 65 ASP cc_start: 0.7099 (t0) cc_final: 0.6749 (t0) REVERT: D 394 TYR cc_start: 0.8906 (m-80) cc_final: 0.8484 (m-80) outliers start: 18 outliers final: 9 residues processed: 107 average time/residue: 0.0857 time to fit residues: 12.3422 Evaluate side-chains 100 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 0.0470 chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 0.0040 chunk 42 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.190336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.161092 restraints weight = 6914.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.165082 restraints weight = 4526.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.167628 restraints weight = 3381.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.169608 restraints weight = 2785.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170736 restraints weight = 2436.135| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6739 Z= 0.115 Angle : 0.514 6.765 9123 Z= 0.271 Chirality : 0.045 0.146 1039 Planarity : 0.003 0.035 1168 Dihedral : 10.800 152.978 904 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.07 % Allowed : 14.94 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.74 (0.29), residues: 840 helix: 1.80 (0.27), residues: 380 sheet: 0.25 (0.44), residues: 133 loop : -0.99 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.007 0.001 TYR A 416 PHE 0.013 0.001 PHE D 381 TRP 0.016 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6739) covalent geometry : angle 0.51386 ( 9123) hydrogen bonds : bond 0.03587 ( 325) hydrogen bonds : angle 4.16718 ( 930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.251 Fit side-chains REVERT: A 123 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7562 (m) REVERT: A 222 ASN cc_start: 0.7868 (m-40) cc_final: 0.7285 (m-40) REVERT: A 305 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8316 (mtp85) REVERT: A 337 ASN cc_start: 0.7626 (p0) cc_final: 0.6921 (m-40) REVERT: A 365 ASN cc_start: 0.7706 (t0) cc_final: 0.7282 (t0) REVERT: A 416 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.5857 (t80) REVERT: D 394 TYR cc_start: 0.8843 (m-80) cc_final: 0.8340 (m-80) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 0.0933 time to fit residues: 12.9503 Evaluate side-chains 97 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.189767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160709 restraints weight = 7018.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164716 restraints weight = 4566.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.167366 restraints weight = 3408.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.169253 restraints weight = 2784.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170347 restraints weight = 2434.274| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6739 Z= 0.119 Angle : 0.534 10.079 9123 Z= 0.276 Chirality : 0.045 0.150 1039 Planarity : 0.003 0.037 1168 Dihedral : 10.603 151.968 904 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.35 % Allowed : 14.25 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.66 (0.29), residues: 840 helix: 1.77 (0.27), residues: 380 sheet: 0.17 (0.44), residues: 133 loop : -1.05 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.007 0.001 TYR A 416 PHE 0.019 0.001 PHE A 97 TRP 0.015 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6739) covalent geometry : angle 0.53370 ( 9123) hydrogen bonds : bond 0.03654 ( 325) hydrogen bonds : angle 4.16585 ( 930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.210 Fit side-chains REVERT: A 110 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 123 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7565 (m) REVERT: A 222 ASN cc_start: 0.7940 (m-40) cc_final: 0.7091 (m-40) REVERT: A 238 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8161 (m-80) REVERT: A 293 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6570 (mt-10) REVERT: A 337 ASN cc_start: 0.7608 (p0) cc_final: 0.6875 (m110) REVERT: A 365 ASN cc_start: 0.7772 (t0) cc_final: 0.7330 (t0) REVERT: A 381 ARG cc_start: 0.7703 (ttp-110) cc_final: 0.7230 (mtm110) REVERT: A 416 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.5934 (t80) REVERT: D 163 MET cc_start: 0.6829 (tpt) cc_final: 0.6462 (tpt) REVERT: D 235 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8695 (p) REVERT: D 394 TYR cc_start: 0.8869 (m-80) cc_final: 0.8342 (m-80) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 0.0951 time to fit residues: 13.2696 Evaluate side-chains 109 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.0070 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.191248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.160334 restraints weight = 7089.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164424 restraints weight = 4677.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167152 restraints weight = 3542.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.168767 restraints weight = 2939.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.170000 restraints weight = 2611.900| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6739 Z= 0.127 Angle : 0.557 10.903 9123 Z= 0.288 Chirality : 0.046 0.144 1039 Planarity : 0.004 0.036 1168 Dihedral : 10.400 153.201 904 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.21 % Allowed : 14.80 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.68 (0.29), residues: 840 helix: 1.79 (0.27), residues: 380 sheet: 0.23 (0.44), residues: 133 loop : -1.07 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 154 TYR 0.007 0.001 TYR A 416 PHE 0.014 0.001 PHE D 381 TRP 0.014 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6739) covalent geometry : angle 0.55745 ( 9123) hydrogen bonds : bond 0.03706 ( 325) hydrogen bonds : angle 4.16664 ( 930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.253 Fit side-chains REVERT: A 110 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7190 (mm-30) REVERT: A 123 THR cc_start: 0.7916 (m) cc_final: 0.7540 (m) REVERT: A 238 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: A 293 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6531 (mt-10) REVERT: A 337 ASN cc_start: 0.7614 (p0) cc_final: 0.6947 (m110) REVERT: A 381 ARG cc_start: 0.7694 (ttp-110) cc_final: 0.7223 (mtm110) REVERT: A 416 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.5952 (t80) REVERT: D 163 MET cc_start: 0.6880 (tpt) cc_final: 0.6483 (tpt) REVERT: D 235 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8740 (p) REVERT: D 394 TYR cc_start: 0.8850 (m-80) cc_final: 0.8322 (m-80) REVERT: D 417 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7127 (mt-10) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 0.0982 time to fit residues: 13.0532 Evaluate side-chains 102 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.186052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157740 restraints weight = 6895.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161265 restraints weight = 4634.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.163744 restraints weight = 3553.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165340 restraints weight = 2995.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166257 restraints weight = 2672.997| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6739 Z= 0.134 Angle : 0.560 11.028 9123 Z= 0.289 Chirality : 0.046 0.147 1039 Planarity : 0.004 0.038 1168 Dihedral : 10.255 156.402 904 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.21 % Allowed : 15.21 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.63 (0.29), residues: 840 helix: 1.75 (0.27), residues: 380 sheet: 0.20 (0.44), residues: 133 loop : -1.10 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 305 TYR 0.008 0.001 TYR A 306 PHE 0.015 0.001 PHE D 381 TRP 0.015 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6739) covalent geometry : angle 0.55965 ( 9123) hydrogen bonds : bond 0.03772 ( 325) hydrogen bonds : angle 4.16889 ( 930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.249 Fit side-chains REVERT: A 110 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 123 THR cc_start: 0.7943 (m) cc_final: 0.7560 (m) REVERT: A 222 ASN cc_start: 0.7903 (m-40) cc_final: 0.7199 (m-40) REVERT: A 238 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: A 293 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6589 (mt-10) REVERT: A 337 ASN cc_start: 0.7635 (p0) cc_final: 0.6941 (m110) REVERT: A 365 ASN cc_start: 0.7897 (t0) cc_final: 0.7655 (t0) REVERT: A 381 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7142 (mtm110) REVERT: A 416 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.5936 (t80) REVERT: D 163 MET cc_start: 0.6957 (tpt) cc_final: 0.6544 (tpt) REVERT: D 174 ASP cc_start: 0.8107 (p0) cc_final: 0.7759 (p0) REVERT: D 235 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8669 (p) REVERT: D 394 TYR cc_start: 0.8893 (m-80) cc_final: 0.8465 (m-80) outliers start: 16 outliers final: 9 residues processed: 107 average time/residue: 0.0831 time to fit residues: 12.0232 Evaluate side-chains 109 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS D 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.193110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162293 restraints weight = 6976.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166351 restraints weight = 4615.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.169063 restraints weight = 3496.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170604 restraints weight = 2901.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172024 restraints weight = 2581.342| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6739 Z= 0.115 Angle : 0.543 6.796 9123 Z= 0.281 Chirality : 0.045 0.140 1039 Planarity : 0.004 0.036 1168 Dihedral : 9.985 157.358 904 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.80 % Allowed : 16.18 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.71 (0.29), residues: 840 helix: 1.83 (0.27), residues: 380 sheet: 0.25 (0.44), residues: 133 loop : -1.08 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 305 TYR 0.007 0.001 TYR A 416 PHE 0.014 0.001 PHE A 313 TRP 0.016 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6739) covalent geometry : angle 0.54254 ( 9123) hydrogen bonds : bond 0.03516 ( 325) hydrogen bonds : angle 4.15885 ( 930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.91 seconds wall clock time: 22 minutes 31.58 seconds (1351.58 seconds total)