Starting phenix.real_space_refine on Sat May 10 17:18:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6v_50241/05_2025/9f6v_50241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6v_50241/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6v_50241/05_2025/9f6v_50241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6v_50241/05_2025/9f6v_50241.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6v_50241/05_2025/9f6v_50241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6v_50241/05_2025/9f6v_50241.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.20, per 1000 atoms: 0.64 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: 1.59 Conformation dependent library (CDL) restraints added in 887.4 milliseconds 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: 0.74 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: 1.91 Time building geometry restraints manager: 1.86 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: 0.380 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.380 Find NCS groups from input model: 0.100 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (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 TRP 0.043 0.007 TRP D 22 HIS 0.010 0.003 HIS D 321 PHE 0.042 0.006 PHE A 313 TYR 0.031 0.006 TYR D 394 ARG 0.008 0.001 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.17422 ( 325) hydrogen bonds : angle 6.92545 ( 930) covalent geometry : bond 0.02345 ( 6739) covalent geometry : angle 1.54918 ( 9123) *********************** 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 : 0.669 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: 0.7351 (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: 0.6290 (tp30) REVERT: D 410 ASN cc_start: 0.6799 (m-40) cc_final: 0.6510 (t0) REVERT: D 417 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6969 (mt-10) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2368 time to fit residues: 54.7249 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.189503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.160235 restraints weight = 6930.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164415 restraints weight = 4450.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167276 restraints weight = 3301.967| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6739 Z= 0.179 Angle : 0.658 7.215 9123 Z= 0.359 Chirality : 0.049 0.183 1039 Planarity : 0.005 0.054 1168 Dihedral : 12.290 165.119 904 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.49 % Allowed : 6.09 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 840 helix: 1.06 (0.27), residues: 361 sheet: 1.24 (0.46), residues: 136 loop : -0.40 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 22 HIS 0.004 0.001 HIS A 260 PHE 0.027 0.002 PHE A 97 TYR 0.012 0.002 TYR A 306 ARG 0.004 0.000 ARG D 239 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 325) hydrogen bonds : angle 4.96151 ( 930) covalent geometry : bond 0.00411 ( 6739) covalent geometry : angle 0.65804 ( 9123) *********************** 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 139 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.689 Fit side-chains REVERT: A 46 ASP cc_start: 0.7409 (t70) cc_final: 0.7208 (t0) REVERT: A 222 ASN cc_start: 0.8063 (m-40) cc_final: 0.7246 (m-40) REVERT: A 367 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7727 (mm-30) outliers start: 18 outliers final: 6 residues processed: 133 average time/residue: 0.1867 time to fit residues: 32.9829 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 : 0.692 ------------------------------------------------------------------------------- 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 70 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS D 36 GLN ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.188653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.159770 restraints weight = 7020.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163826 restraints weight = 4549.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.166574 restraints weight = 3383.383| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6739 Z= 0.134 Angle : 0.550 5.823 9123 Z= 0.297 Chirality : 0.046 0.165 1039 Planarity : 0.004 0.048 1168 Dihedral : 11.687 160.533 904 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.66 % Allowed : 9.54 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 840 helix: 1.39 (0.27), residues: 368 sheet: 0.78 (0.46), residues: 144 loop : -0.49 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 22 HIS 0.003 0.001 HIS A 104 PHE 0.015 0.001 PHE A 97 TYR 0.008 0.001 TYR A 306 ARG 0.003 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 325) hydrogen bonds : angle 4.57472 ( 930) covalent geometry : bond 0.00309 ( 6739) covalent geometry : angle 0.55032 ( 9123) *********************** 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 111 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.721 Fit side-chains REVERT: A 222 ASN cc_start: 0.8063 (m-40) cc_final: 0.7457 (m-40) REVERT: D 163 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6939 (ttt) REVERT: D 192 SER cc_start: 0.7696 (m) cc_final: 0.7495 (p) REVERT: D 394 TYR cc_start: 0.8930 (m-80) cc_final: 0.8662 (m-80) outliers start: 12 outliers final: 8 residues processed: 107 average time/residue: 0.1892 time to fit residues: 27.4299 Evaluate side-chains 92 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 D residue 118 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 237 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 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 0.0470 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.189413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.160585 restraints weight = 7118.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.164611 restraints weight = 4595.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167437 restraints weight = 3414.888| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4432 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= 0.115 Angle : 0.509 6.353 9123 Z= 0.273 Chirality : 0.045 0.163 1039 Planarity : 0.004 0.040 1168 Dihedral : 11.337 158.367 904 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.21 % Allowed : 10.10 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 840 helix: 1.45 (0.26), residues: 384 sheet: 0.83 (0.46), residues: 135 loop : -0.70 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 PHE 0.012 0.001 PHE A 313 TYR 0.013 0.001 TYR A 191 ARG 0.003 0.000 ARG D 239 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 325) hydrogen bonds : angle 4.33509 ( 930) covalent geometry : bond 0.00261 ( 6739) covalent geometry : angle 0.50910 ( 9123) *********************** 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 114 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.768 Fit side-chains REVERT: A 123 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7508 (m) REVERT: A 222 ASN cc_start: 0.8013 (m-40) cc_final: 0.7425 (m-40) REVERT: A 239 SER cc_start: 0.9206 (t) cc_final: 0.8974 (p) REVERT: A 305 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.8379 (mtp85) REVERT: A 416 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6269 (t80) REVERT: D 163 MET cc_start: 0.7118 (ttt) cc_final: 0.6810 (ttt) REVERT: D 192 SER cc_start: 0.7826 (m) cc_final: 0.7595 (p) REVERT: D 394 TYR cc_start: 0.8888 (m-80) cc_final: 0.8589 (m-80) outliers start: 16 outliers final: 7 residues processed: 107 average time/residue: 0.1826 time to fit residues: 26.4198 Evaluate side-chains 96 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN D 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153050 restraints weight = 7112.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156746 restraints weight = 4692.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159400 restraints weight = 3571.218| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6739 Z= 0.219 Angle : 0.605 6.312 9123 Z= 0.323 Chirality : 0.049 0.159 1039 Planarity : 0.004 0.046 1168 Dihedral : 11.385 159.540 904 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.49 % Allowed : 11.89 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 840 helix: 1.41 (0.26), residues: 377 sheet: 0.53 (0.45), residues: 135 loop : -0.93 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 338 HIS 0.004 0.001 HIS A 133 PHE 0.022 0.002 PHE D 381 TYR 0.015 0.002 TYR D 33 ARG 0.003 0.000 ARG D 60 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 325) hydrogen bonds : angle 4.45953 ( 930) covalent geometry : bond 0.00535 ( 6739) covalent geometry : angle 0.60500 ( 9123) *********************** 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 118 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.693 Fit side-chains REVERT: A 25 ILE cc_start: 0.7592 (tt) cc_final: 0.7267 (tt) REVERT: A 123 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7722 (m) REVERT: A 222 ASN cc_start: 0.8074 (m-40) cc_final: 0.7311 (m-40) REVERT: A 293 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6577 (mt-10) REVERT: D 163 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6984 (ttt) REVERT: D 192 SER cc_start: 0.7866 (m) cc_final: 0.7645 (p) REVERT: D 304 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7725 (tm-30) REVERT: D 356 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8158 (mmtp) REVERT: D 394 TYR cc_start: 0.9001 (m-80) cc_final: 0.8747 (m-80) outliers start: 18 outliers final: 10 residues processed: 110 average time/residue: 0.1848 time to fit residues: 27.5820 Evaluate side-chains 100 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 281 THR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 266 THR 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 9 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.186849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156581 restraints weight = 7016.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160529 restraints weight = 4693.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163174 restraints weight = 3565.035| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4905 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= 0.145 Angle : 0.539 6.679 9123 Z= 0.287 Chirality : 0.046 0.159 1039 Planarity : 0.004 0.041 1168 Dihedral : 11.097 155.404 904 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.90 % Allowed : 13.14 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.29), residues: 840 helix: 1.54 (0.27), residues: 380 sheet: 0.26 (0.44), residues: 135 loop : -1.06 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 PHE 0.023 0.001 PHE A 97 TYR 0.014 0.001 TYR A 191 ARG 0.002 0.000 ARG D 239 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 325) hydrogen bonds : angle 4.28561 ( 930) covalent geometry : bond 0.00347 ( 6739) covalent geometry : angle 0.53879 ( 9123) *********************** 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 116 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.680 Fit side-chains REVERT: A 25 ILE cc_start: 0.7606 (tt) cc_final: 0.7259 (tt) REVERT: A 107 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6557 (mm-30) REVERT: A 123 THR cc_start: 0.8022 (m) cc_final: 0.7692 (m) REVERT: A 222 ASN cc_start: 0.8022 (m-40) cc_final: 0.7442 (m-40) REVERT: D 304 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 356 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8155 (mmtp) REVERT: D 394 TYR cc_start: 0.8927 (m-80) cc_final: 0.8586 (m-80) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 0.1996 time to fit residues: 28.1019 Evaluate side-chains 96 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 351 THR 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 64 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.188483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.158222 restraints weight = 7026.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162141 restraints weight = 4660.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164558 restraints weight = 3528.441| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6739 Z= 0.127 Angle : 0.524 6.773 9123 Z= 0.277 Chirality : 0.046 0.149 1039 Planarity : 0.004 0.038 1168 Dihedral : 10.852 153.836 904 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.63 % Allowed : 13.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.29), residues: 840 helix: 1.69 (0.27), residues: 380 sheet: 0.12 (0.44), residues: 135 loop : -1.12 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 PHE 0.013 0.001 PHE D 381 TYR 0.013 0.001 TYR A 191 ARG 0.002 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 325) hydrogen bonds : angle 4.21248 ( 930) covalent geometry : bond 0.00300 ( 6739) covalent geometry : angle 0.52401 ( 9123) *********************** 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 114 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.698 Fit side-chains REVERT: A 25 ILE cc_start: 0.7598 (tt) cc_final: 0.7222 (tt) REVERT: A 123 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7659 (m) REVERT: A 222 ASN cc_start: 0.7942 (m-40) cc_final: 0.7394 (m-40) REVERT: A 293 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6583 (mt-10) REVERT: D 123 ASP cc_start: 0.6864 (t0) cc_final: 0.6499 (m-30) REVERT: D 304 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 394 TYR cc_start: 0.8887 (m-80) cc_final: 0.8454 (m-80) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 0.1892 time to fit residues: 26.3848 Evaluate side-chains 104 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 131 LEU 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 D residue 105 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 279 HIS Chi-restraints excluded: chain D residue 351 THR 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 79 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.188442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157836 restraints weight = 7052.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161339 restraints weight = 4698.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164329 restraints weight = 3606.908| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5173 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= 0.129 Angle : 0.527 6.474 9123 Z= 0.278 Chirality : 0.046 0.153 1039 Planarity : 0.004 0.037 1168 Dihedral : 10.623 153.401 904 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.07 % Allowed : 14.38 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 840 helix: 1.73 (0.27), residues: 380 sheet: 0.03 (0.44), residues: 135 loop : -1.16 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 PHE 0.017 0.001 PHE A 97 TYR 0.013 0.001 TYR A 191 ARG 0.002 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 325) hydrogen bonds : angle 4.18425 ( 930) covalent geometry : bond 0.00306 ( 6739) covalent geometry : angle 0.52690 ( 9123) *********************** 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 107 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 25 ILE cc_start: 0.7606 (tt) cc_final: 0.7234 (tt) REVERT: A 123 THR cc_start: 0.7996 (m) cc_final: 0.7672 (m) REVERT: A 381 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7161 (mtm110) REVERT: D 123 ASP cc_start: 0.6875 (t0) cc_final: 0.6538 (m-30) REVERT: D 174 ASP cc_start: 0.8085 (p0) cc_final: 0.7842 (p0) REVERT: D 304 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7716 (tm-30) REVERT: D 394 TYR cc_start: 0.8897 (m-80) cc_final: 0.8464 (m-80) outliers start: 15 outliers final: 12 residues processed: 101 average time/residue: 0.2131 time to fit residues: 28.2682 Evaluate side-chains 100 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 265 SER 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 237 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 279 HIS Chi-restraints excluded: chain D residue 351 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 50 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.187410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156881 restraints weight = 7016.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.160851 restraints weight = 4649.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163319 restraints weight = 3526.924| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6739 Z= 0.135 Angle : 0.538 6.734 9123 Z= 0.283 Chirality : 0.046 0.145 1039 Planarity : 0.004 0.036 1168 Dihedral : 10.440 153.857 904 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.35 % Allowed : 14.52 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.29), residues: 840 helix: 1.73 (0.27), residues: 380 sheet: 0.08 (0.44), residues: 133 loop : -1.21 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 PHE 0.014 0.001 PHE D 381 TYR 0.013 0.001 TYR A 191 ARG 0.006 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 325) hydrogen bonds : angle 4.18287 ( 930) covalent geometry : bond 0.00321 ( 6739) covalent geometry : angle 0.53809 ( 9123) *********************** 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 107 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 25 ILE cc_start: 0.7589 (tt) cc_final: 0.7184 (tt) REVERT: A 123 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7674 (m) REVERT: A 238 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: A 416 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.5839 (t80) REVERT: D 123 ASP cc_start: 0.6858 (t0) cc_final: 0.6527 (m-30) REVERT: D 174 ASP cc_start: 0.8056 (p0) cc_final: 0.7778 (p0) REVERT: D 304 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 394 TYR cc_start: 0.8886 (m-80) cc_final: 0.8446 (m-80) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.1871 time to fit residues: 25.1447 Evaluate side-chains 104 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 131 LEU 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 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 237 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 279 HIS Chi-restraints excluded: chain D residue 351 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 45 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 48 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.193786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163209 restraints weight = 7058.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.167208 restraints weight = 4661.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.169992 restraints weight = 3529.790| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6739 Z= 0.108 Angle : 0.526 8.730 9123 Z= 0.274 Chirality : 0.045 0.165 1039 Planarity : 0.003 0.033 1168 Dihedral : 10.012 153.215 904 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.24 % Allowed : 15.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.29), residues: 840 helix: 1.81 (0.27), residues: 380 sheet: 0.23 (0.44), residues: 133 loop : -1.14 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 22 HIS 0.002 0.000 HIS A 104 PHE 0.014 0.001 PHE A 313 TYR 0.013 0.001 TYR A 191 ARG 0.006 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 325) hydrogen bonds : angle 4.15646 ( 930) covalent geometry : bond 0.00245 ( 6739) covalent geometry : angle 0.52616 ( 9123) ********************** 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 114 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 25 ILE cc_start: 0.7563 (tt) cc_final: 0.7179 (tt) REVERT: A 123 THR cc_start: 0.7930 (m) cc_final: 0.7603 (m) REVERT: A 238 PHE cc_start: 0.8413 (m-80) cc_final: 0.8043 (m-80) REVERT: A 337 ASN cc_start: 0.7724 (p0) cc_final: 0.6965 (m110) REVERT: A 381 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.7087 (mtm110) REVERT: A 416 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.5989 (t80) REVERT: A 418 LYS cc_start: 0.8113 (pttt) cc_final: 0.7863 (pttp) REVERT: D 65 ASP cc_start: 0.6909 (t0) cc_final: 0.6419 (t70) REVERT: D 123 ASP cc_start: 0.6839 (t0) cc_final: 0.6447 (m-30) REVERT: D 174 ASP cc_start: 0.8026 (p0) cc_final: 0.7727 (p0) REVERT: D 304 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7675 (tm-30) REVERT: D 394 TYR cc_start: 0.8844 (m-80) cc_final: 0.8302 (m-80) REVERT: D 417 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7009 (mt-10) outliers start: 9 outliers final: 7 residues processed: 109 average time/residue: 0.2100 time to fit residues: 30.1619 Evaluate side-chains 107 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 351 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 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.190886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160450 restraints weight = 7027.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.164320 restraints weight = 4671.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.167031 restraints weight = 3553.300| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5498 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 : 0.557 10.562 9123 Z= 0.284 Chirality : 0.046 0.142 1039 Planarity : 0.003 0.033 1168 Dihedral : 9.773 154.147 904 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.66 % Allowed : 16.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.29), residues: 840 helix: 1.80 (0.27), residues: 380 sheet: 0.28 (0.45), residues: 126 loop : -1.04 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 22 HIS 0.002 0.001 HIS A 104 PHE 0.013 0.001 PHE D 381 TYR 0.021 0.001 TYR D 395 ARG 0.006 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 325) hydrogen bonds : angle 4.13175 ( 930) covalent geometry : bond 0.00288 ( 6739) covalent geometry : angle 0.55743 ( 9123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2226.26 seconds wall clock time: 40 minutes 5.69 seconds (2405.69 seconds total)