Starting phenix.real_space_refine on Wed Feb 4 10:37:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i8q_52731/02_2026/9i8q_52731.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i8q_52731/02_2026/9i8q_52731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i8q_52731/02_2026/9i8q_52731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i8q_52731/02_2026/9i8q_52731.map" model { file = "/net/cci-nas-00/data/ceres_data/9i8q_52731/02_2026/9i8q_52731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i8q_52731/02_2026/9i8q_52731.cif" } resolution = 2.93 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= 0.003 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6432 2.51 5 N 1677 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10092 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Chain: "B" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Chain: "C" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Time building chain proxies: 2.75, per 1000 atoms: 0.27 Number of scatterers: 10092 At special positions: 0 Unit cell: (102.9, 97.65, 106.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1920 8.00 N 1677 7.00 C 6432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 92 " distance=2.02 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 390.6 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 21 sheets defined 22.4% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 removed outlier: 4.126A pdb=" N ALA A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 52 " --> pdb=" O HIS A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 52' Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.518A pdb=" N ASP A 178 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 179 " --> pdb=" O LEU A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 179' Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 214 through 218 removed outlier: 4.121A pdb=" N LYS A 217 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 218 " --> pdb=" O GLY A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 218' Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.588A pdb=" N ARG A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 294 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.657A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'B' and resid 48 through 51 removed outlier: 4.080A pdb=" N ALA B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.501A pdb=" N SER B 179 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.541A pdb=" N SER B 197 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.530A pdb=" N ARG B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.786A pdb=" N LEU B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.787A pdb=" N ALA C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 52 " --> pdb=" O HIS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 101 removed outlier: 3.524A pdb=" N SER C 95 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.523A pdb=" N SER C 197 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.674A pdb=" N ARG C 249 " --> pdb=" O PHE C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 275 through 294 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.614A pdb=" N LEU C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 382 through 387 Processing helix chain 'C' and resid 393 through 398 removed outlier: 3.648A pdb=" N HIS C 397 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 398 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.874A pdb=" N PHE A 2 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 206 removed outlier: 5.425A pdb=" N MET A 239 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N TRP A 227 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 85 removed outlier: 3.585A pdb=" N ARG A 83 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 61 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 85 removed outlier: 3.585A pdb=" N ARG A 83 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 61 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'B' and resid 213 through 214 removed outlier: 5.125A pdb=" N MET B 239 " --> pdb=" O TRP B 227 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N TRP B 227 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'B' and resid 77 through 85 removed outlier: 4.172A pdb=" N ALA B 61 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 122 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 77 through 85 removed outlier: 4.172A pdb=" N ALA B 61 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 361 through 363 Processing sheet with id=AB6, first strand: chain 'C' and resid 2 through 7 removed outlier: 4.009A pdb=" N PHE C 2 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 335 " --> pdb=" O PHE C 2 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AB8, first strand: chain 'C' and resid 213 through 214 removed outlier: 4.590A pdb=" N MET C 239 " --> pdb=" O TRP C 227 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TRP C 227 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 123 through 131 removed outlier: 3.909A pdb=" N THR C 166 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 123 through 131 removed outlier: 4.104A pdb=" N PHE C 424 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AC3, first strand: chain 'C' and resid 361 through 363 393 hydrogen bonds defined for protein. 1008 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: 1.88 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1659 1.30 - 1.43: 2895 1.43 - 1.55: 5755 1.55 - 1.68: 2 1.68 - 1.81: 90 Bond restraints: 10401 Sorted by residual: bond pdb=" C PRO C 338 " pdb=" O PRO C 338 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.30e-02 5.92e+03 2.61e+01 bond pdb=" N ALA C 337 " pdb=" CA ALA C 337 " ideal model delta sigma weight residual 1.455 1.489 -0.035 9.60e-03 1.09e+04 1.30e+01 bond pdb=" CA ALA C 337 " pdb=" CB ALA C 337 " ideal model delta sigma weight residual 1.535 1.488 0.047 1.36e-02 5.41e+03 1.19e+01 bond pdb=" N ILE C 339 " pdb=" CA ILE C 339 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.21e-02 6.83e+03 6.57e+00 bond pdb=" N SER A 27 " pdb=" CA SER A 27 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.27e-02 6.20e+03 6.21e+00 ... (remaining 10396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 13837 2.15 - 4.31: 286 4.31 - 6.46: 27 6.46 - 8.62: 10 8.62 - 10.77: 3 Bond angle restraints: 14163 Sorted by residual: angle pdb=" C ILE C 339 " pdb=" N LEU C 340 " pdb=" CA LEU C 340 " ideal model delta sigma weight residual 123.00 131.48 -8.48 1.41e+00 5.03e-01 3.62e+01 angle pdb=" N TRP A 357 " pdb=" CA TRP A 357 " pdb=" C TRP A 357 " ideal model delta sigma weight residual 108.42 116.93 -8.51 1.54e+00 4.22e-01 3.06e+01 angle pdb=" C LEU A 356 " pdb=" N TRP A 357 " pdb=" CA TRP A 357 " ideal model delta sigma weight residual 121.91 111.14 10.77 2.03e+00 2.43e-01 2.82e+01 angle pdb=" C VAL B 267 " pdb=" N ASP B 268 " pdb=" CA ASP B 268 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C PRO C 418 " pdb=" CA PRO C 418 " pdb=" CB PRO C 418 " ideal model delta sigma weight residual 111.12 104.59 6.53 1.29e+00 6.01e-01 2.56e+01 ... (remaining 14158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5189 17.57 - 35.14: 666 35.14 - 52.71: 209 52.71 - 70.28: 47 70.28 - 87.85: 21 Dihedral angle restraints: 6132 sinusoidal: 2433 harmonic: 3699 Sorted by residual: dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual 93.00 174.44 -81.44 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS C 68 " pdb=" SG CYS C 68 " pdb=" SG CYS C 114 " pdb=" CB CYS C 114 " ideal model delta sinusoidal sigma weight residual -86.00 -10.83 -75.17 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS C 59 " pdb=" SG CYS C 59 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 166.63 -73.63 1 1.00e+01 1.00e-02 6.89e+01 ... (remaining 6129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1124 0.048 - 0.096: 275 0.096 - 0.145: 88 0.145 - 0.193: 10 0.193 - 0.241: 3 Chirality restraints: 1500 Sorted by residual: chirality pdb=" CA CYS B 59 " pdb=" N CYS B 59 " pdb=" C CYS B 59 " pdb=" CB CYS B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA GLU A 355 " pdb=" N GLU A 355 " pdb=" C GLU A 355 " pdb=" CB GLU A 355 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU B 384 " pdb=" CB LEU B 384 " pdb=" CD1 LEU B 384 " pdb=" CD2 LEU B 384 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 1497 not shown) Planarity restraints: 1821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 336 " -0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C ALA C 336 " 0.083 2.00e-02 2.50e+03 pdb=" O ALA C 336 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA C 337 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 337 " -0.062 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO A 338 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 337 " 0.062 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO B 338 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " 0.049 5.00e-02 4.00e+02 ... (remaining 1818 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 752 2.74 - 3.28: 10284 3.28 - 3.82: 17207 3.82 - 4.36: 21528 4.36 - 4.90: 36492 Nonbonded interactions: 86263 Sorted by model distance: nonbonded pdb=" NE1 TRP B 357 " pdb=" O ASP B 359 " model vdw 2.194 3.120 nonbonded pdb=" OE1 GLN B 285 " pdb=" OG SER B 289 " model vdw 2.205 3.040 nonbonded pdb=" NE1 TRP C 357 " pdb=" O ASP C 359 " model vdw 2.219 3.120 nonbonded pdb=" OG SER C 62 " pdb=" O ARG C 83 " model vdw 2.265 3.040 nonbonded pdb=" O SER B 207 " pdb=" NH2 ARG B 332 " model vdw 2.267 3.120 ... (remaining 86258 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.100 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.004 0.106 10419 Z= 0.211 Angle : 0.733 10.771 14199 Z= 0.415 Chirality : 0.048 0.241 1500 Planarity : 0.006 0.091 1821 Dihedral : 17.976 87.851 3708 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.47 % Favored : 91.67 % Rotamer: Outliers : 2.69 % Allowed : 28.58 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1272 helix: 0.09 (0.37), residues: 195 sheet: -1.33 (0.35), residues: 183 loop : -0.72 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 83 TYR 0.032 0.002 TYR A 380 PHE 0.012 0.001 PHE A 326 TRP 0.027 0.001 TRP A 236 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00419 (10401) covalent geometry : angle 0.72901 (14163) SS BOND : bond 0.00220 ( 18) SS BOND : angle 1.65439 ( 36) hydrogen bonds : bond 0.17979 ( 368) hydrogen bonds : angle 8.21540 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8206 (pttt) cc_final: 0.7860 (pttm) REVERT: A 358 ASP cc_start: 0.7552 (m-30) cc_final: 0.7346 (m-30) REVERT: B 200 LYS cc_start: 0.7800 (mptt) cc_final: 0.7473 (mptt) REVERT: C 406 GLU cc_start: 0.7981 (tt0) cc_final: 0.7751 (tt0) outliers start: 30 outliers final: 19 residues processed: 163 average time/residue: 0.4466 time to fit residues: 78.9217 Evaluate side-chains 152 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 49 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.198749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145517 restraints weight = 11211.226| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.20 r_work: 0.3511 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10419 Z= 0.156 Angle : 0.646 9.560 14199 Z= 0.335 Chirality : 0.046 0.166 1500 Planarity : 0.006 0.067 1821 Dihedral : 6.517 54.206 1396 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.00 % Favored : 92.30 % Rotamer: Outliers : 4.57 % Allowed : 25.99 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1272 helix: 0.75 (0.36), residues: 201 sheet: -1.04 (0.37), residues: 168 loop : -0.74 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 277 TYR 0.024 0.002 TYR A 380 PHE 0.014 0.001 PHE A 210 TRP 0.012 0.001 TRP A 236 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00362 (10401) covalent geometry : angle 0.64176 (14163) SS BOND : bond 0.00216 ( 18) SS BOND : angle 1.57350 ( 36) hydrogen bonds : bond 0.04322 ( 368) hydrogen bonds : angle 6.47514 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.319 Fit side-chains REVERT: A 174 LYS cc_start: 0.8131 (pttt) cc_final: 0.7730 (pttm) REVERT: A 274 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7547 (t0) REVERT: B 11 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7817 (pttt) REVERT: B 200 LYS cc_start: 0.7996 (mptt) cc_final: 0.7762 (mptt) REVERT: B 238 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6818 (pp20) REVERT: C 274 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7115 (m-30) outliers start: 51 outliers final: 16 residues processed: 184 average time/residue: 0.4147 time to fit residues: 83.0978 Evaluate side-chains 147 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 399 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 49 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.197505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143979 restraints weight = 11212.303| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.20 r_work: 0.3490 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10419 Z= 0.168 Angle : 0.640 11.475 14199 Z= 0.329 Chirality : 0.046 0.157 1500 Planarity : 0.005 0.067 1821 Dihedral : 6.138 54.253 1375 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.39 % Favored : 91.90 % Rotamer: Outliers : 3.76 % Allowed : 27.42 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.23), residues: 1272 helix: 0.84 (0.36), residues: 201 sheet: -1.06 (0.37), residues: 168 loop : -0.71 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 83 TYR 0.023 0.002 TYR A 385 PHE 0.016 0.001 PHE A 210 TRP 0.010 0.001 TRP A 236 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00389 (10401) covalent geometry : angle 0.63539 (14163) SS BOND : bond 0.00225 ( 18) SS BOND : angle 1.58805 ( 36) hydrogen bonds : bond 0.04067 ( 368) hydrogen bonds : angle 6.31074 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.391 Fit side-chains REVERT: A 63 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6716 (mtpp) REVERT: A 174 LYS cc_start: 0.8160 (pttt) cc_final: 0.7739 (pttm) REVERT: A 195 LEU cc_start: 0.7561 (mm) cc_final: 0.7311 (mm) REVERT: B 11 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7825 (pttt) REVERT: B 45 MET cc_start: 0.8227 (mtp) cc_final: 0.7841 (mtm) REVERT: B 200 LYS cc_start: 0.8012 (mptt) cc_final: 0.7738 (mptt) REVERT: B 238 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6865 (pp20) REVERT: B 274 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7694 (t0) REVERT: B 354 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7159 (ttm-80) REVERT: B 391 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6050 (tpt) REVERT: C 78 ILE cc_start: 0.4279 (OUTLIER) cc_final: 0.3997 (tt) REVERT: C 274 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: C 384 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8028 (mm) outliers start: 42 outliers final: 15 residues processed: 178 average time/residue: 0.4240 time to fit residues: 82.1451 Evaluate side-chains 160 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 384 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 83 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 49 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.199372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146216 restraints weight = 11321.742| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.21 r_work: 0.3518 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10419 Z= 0.134 Angle : 0.618 12.256 14199 Z= 0.315 Chirality : 0.045 0.159 1500 Planarity : 0.005 0.066 1821 Dihedral : 5.966 55.511 1374 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.39 % Favored : 92.06 % Rotamer: Outliers : 4.03 % Allowed : 26.88 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.23), residues: 1272 helix: 0.89 (0.36), residues: 204 sheet: -0.96 (0.37), residues: 168 loop : -0.65 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 83 TYR 0.021 0.002 TYR A 385 PHE 0.016 0.001 PHE A 210 TRP 0.010 0.001 TRP A 236 HIS 0.008 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00309 (10401) covalent geometry : angle 0.61470 (14163) SS BOND : bond 0.00187 ( 18) SS BOND : angle 1.37140 ( 36) hydrogen bonds : bond 0.03707 ( 368) hydrogen bonds : angle 6.13298 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.312 Fit side-chains REVERT: A 63 LYS cc_start: 0.7132 (mttm) cc_final: 0.6643 (mtpp) REVERT: A 174 LYS cc_start: 0.8104 (pttt) cc_final: 0.7690 (pttm) REVERT: A 195 LEU cc_start: 0.7530 (mm) cc_final: 0.7290 (mm) REVERT: A 274 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7541 (t0) REVERT: B 11 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7816 (pttt) REVERT: B 45 MET cc_start: 0.8321 (mtp) cc_final: 0.7950 (mtm) REVERT: B 200 LYS cc_start: 0.8017 (mptt) cc_final: 0.7736 (mptt) REVERT: B 238 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6861 (pp20) REVERT: B 274 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7634 (t0) REVERT: B 354 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7205 (ttm-80) REVERT: B 391 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6003 (tpt) REVERT: C 78 ILE cc_start: 0.4256 (OUTLIER) cc_final: 0.3980 (tt) REVERT: C 274 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: C 384 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7973 (mm) REVERT: C 386 MET cc_start: 0.7535 (mmm) cc_final: 0.7321 (mmm) REVERT: C 406 GLU cc_start: 0.8408 (tt0) cc_final: 0.8186 (tt0) outliers start: 45 outliers final: 16 residues processed: 186 average time/residue: 0.3894 time to fit residues: 79.0624 Evaluate side-chains 160 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 399 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 0.0050 chunk 53 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.196547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142080 restraints weight = 11210.525| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.20 r_work: 0.3460 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10419 Z= 0.190 Angle : 0.658 13.258 14199 Z= 0.335 Chirality : 0.046 0.167 1500 Planarity : 0.006 0.067 1821 Dihedral : 5.923 45.965 1374 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.63 % Favored : 91.82 % Rotamer: Outliers : 4.39 % Allowed : 27.24 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1272 helix: 0.73 (0.36), residues: 204 sheet: -0.85 (0.37), residues: 162 loop : -0.56 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.025 0.002 TYR A 385 PHE 0.016 0.001 PHE C 210 TRP 0.010 0.001 TRP A 236 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00442 (10401) covalent geometry : angle 0.65317 (14163) SS BOND : bond 0.00289 ( 18) SS BOND : angle 1.65949 ( 36) hydrogen bonds : bond 0.03881 ( 368) hydrogen bonds : angle 6.17903 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.329 Fit side-chains REVERT: A 63 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6653 (mtpp) REVERT: A 174 LYS cc_start: 0.8186 (pttt) cc_final: 0.7754 (pttm) REVERT: A 195 LEU cc_start: 0.7641 (mm) cc_final: 0.7428 (mm) REVERT: A 274 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7663 (t70) REVERT: A 346 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7348 (mmm) REVERT: B 45 MET cc_start: 0.8377 (mtp) cc_final: 0.8003 (mtm) REVERT: B 200 LYS cc_start: 0.8010 (mptt) cc_final: 0.7711 (mptt) REVERT: B 274 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7705 (t0) REVERT: B 354 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7219 (ttm-80) REVERT: B 391 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6287 (tpt) REVERT: C 78 ILE cc_start: 0.4161 (OUTLIER) cc_final: 0.3925 (tt) REVERT: C 83 ARG cc_start: 0.7931 (pmm-80) cc_final: 0.7614 (pmm-80) REVERT: C 184 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6928 (mmt) REVERT: C 212 TYR cc_start: 0.8748 (t80) cc_final: 0.8540 (t80) REVERT: C 328 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8959 (t) REVERT: C 384 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8123 (mm) REVERT: C 386 MET cc_start: 0.7870 (mmm) cc_final: 0.7530 (mmm) outliers start: 49 outliers final: 22 residues processed: 180 average time/residue: 0.4028 time to fit residues: 79.0145 Evaluate side-chains 162 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 399 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 122 optimal weight: 0.3980 chunk 120 optimal weight: 0.0010 chunk 110 optimal weight: 0.0010 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS C 8 HIS C 49 HIS C 309 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.200849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.147640 restraints weight = 11278.666| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.22 r_work: 0.3528 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10419 Z= 0.114 Angle : 0.617 13.253 14199 Z= 0.314 Chirality : 0.045 0.172 1500 Planarity : 0.005 0.067 1821 Dihedral : 5.700 47.517 1374 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.08 % Favored : 92.37 % Rotamer: Outliers : 3.49 % Allowed : 28.32 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1272 helix: 0.98 (0.36), residues: 204 sheet: -0.76 (0.37), residues: 162 loop : -0.51 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 83 TYR 0.019 0.002 TYR A 385 PHE 0.015 0.001 PHE A 210 TRP 0.011 0.001 TRP A 236 HIS 0.008 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00260 (10401) covalent geometry : angle 0.61336 (14163) SS BOND : bond 0.00204 ( 18) SS BOND : angle 1.44209 ( 36) hydrogen bonds : bond 0.03530 ( 368) hydrogen bonds : angle 6.04239 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.254 Fit side-chains REVERT: A 63 LYS cc_start: 0.7105 (mttm) cc_final: 0.6600 (mtpp) REVERT: A 174 LYS cc_start: 0.8162 (pttt) cc_final: 0.7728 (pttm) REVERT: A 195 LEU cc_start: 0.7598 (mm) cc_final: 0.7394 (mm) REVERT: A 274 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7454 (t70) REVERT: A 346 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7439 (mmm) REVERT: B 45 MET cc_start: 0.8332 (mtp) cc_final: 0.8022 (mtm) REVERT: B 83 ARG cc_start: 0.8349 (mtt-85) cc_final: 0.7828 (mpt-90) REVERT: B 200 LYS cc_start: 0.7957 (mptt) cc_final: 0.7691 (mptt) REVERT: B 238 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6894 (pp20) REVERT: B 274 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7673 (t0) REVERT: B 354 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7175 (ttm-80) REVERT: B 391 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.5987 (tpt) REVERT: C 78 ILE cc_start: 0.4120 (OUTLIER) cc_final: 0.3843 (tt) REVERT: C 83 ARG cc_start: 0.7836 (pmm-80) cc_final: 0.7422 (pmm-80) REVERT: C 184 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6848 (mmt) REVERT: C 274 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: C 328 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8924 (t) REVERT: C 386 MET cc_start: 0.7742 (mmm) cc_final: 0.7408 (mmm) REVERT: C 406 GLU cc_start: 0.8398 (tt0) cc_final: 0.8189 (tt0) outliers start: 39 outliers final: 17 residues processed: 174 average time/residue: 0.4284 time to fit residues: 80.7209 Evaluate side-chains 153 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 177 CYS Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 399 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS C 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.197467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142980 restraints weight = 11109.992| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.23 r_work: 0.3474 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10419 Z= 0.183 Angle : 0.645 13.839 14199 Z= 0.328 Chirality : 0.046 0.178 1500 Planarity : 0.005 0.067 1821 Dihedral : 5.749 47.676 1372 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.70 % Favored : 91.75 % Rotamer: Outliers : 4.12 % Allowed : 28.05 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.23), residues: 1272 helix: 0.85 (0.36), residues: 204 sheet: -0.79 (0.36), residues: 168 loop : -0.55 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.022 0.002 TYR A 385 PHE 0.016 0.001 PHE C 210 TRP 0.013 0.001 TRP A 236 HIS 0.013 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00426 (10401) covalent geometry : angle 0.64183 (14163) SS BOND : bond 0.00250 ( 18) SS BOND : angle 1.50442 ( 36) hydrogen bonds : bond 0.03753 ( 368) hydrogen bonds : angle 6.05119 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.322 Fit side-chains REVERT: A 63 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6625 (mtpp) REVERT: A 174 LYS cc_start: 0.8199 (pttt) cc_final: 0.7767 (pttm) REVERT: A 274 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7517 (t70) REVERT: B 45 MET cc_start: 0.8381 (mtp) cc_final: 0.8118 (mtm) REVERT: B 200 LYS cc_start: 0.7969 (mptt) cc_final: 0.7670 (mptt) REVERT: B 238 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6938 (pp20) REVERT: B 274 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 354 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7273 (ttm-80) REVERT: B 391 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6210 (tpt) REVERT: C 78 ILE cc_start: 0.4153 (OUTLIER) cc_final: 0.3880 (tt) REVERT: C 83 ARG cc_start: 0.7895 (pmm-80) cc_final: 0.7490 (pmm-80) REVERT: C 184 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6900 (mmt) REVERT: C 328 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8910 (t) REVERT: C 386 MET cc_start: 0.7806 (mmm) cc_final: 0.7582 (mmm) REVERT: C 391 MET cc_start: 0.7585 (mmt) cc_final: 0.7252 (mmt) REVERT: C 406 GLU cc_start: 0.8418 (tt0) cc_final: 0.8200 (tt0) outliers start: 46 outliers final: 17 residues processed: 170 average time/residue: 0.4465 time to fit residues: 82.0866 Evaluate side-chains 159 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 177 CYS Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 328 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.200397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147572 restraints weight = 11195.330| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.19 r_work: 0.3532 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10419 Z= 0.122 Angle : 0.619 13.940 14199 Z= 0.313 Chirality : 0.045 0.195 1500 Planarity : 0.005 0.067 1821 Dihedral : 5.613 48.594 1372 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.39 % Favored : 92.06 % Rotamer: Outliers : 3.49 % Allowed : 28.67 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1272 helix: 0.98 (0.36), residues: 204 sheet: -0.71 (0.37), residues: 168 loop : -0.51 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 83 TYR 0.020 0.002 TYR A 385 PHE 0.015 0.001 PHE A 210 TRP 0.016 0.001 TRP C 236 HIS 0.008 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00280 (10401) covalent geometry : angle 0.61658 (14163) SS BOND : bond 0.00201 ( 18) SS BOND : angle 1.28882 ( 36) hydrogen bonds : bond 0.03521 ( 368) hydrogen bonds : angle 5.92421 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.396 Fit side-chains REVERT: A 63 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6623 (mtpp) REVERT: A 174 LYS cc_start: 0.8182 (pttt) cc_final: 0.7748 (pttm) REVERT: A 274 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7352 (t0) REVERT: A 346 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7422 (mmm) REVERT: A 412 ASP cc_start: 0.7569 (m-30) cc_final: 0.7290 (m-30) REVERT: B 200 LYS cc_start: 0.7984 (mptt) cc_final: 0.7709 (mptt) REVERT: B 238 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6930 (pp20) REVERT: B 354 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7200 (ttm-80) REVERT: B 391 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5953 (tpt) REVERT: C 83 ARG cc_start: 0.7829 (pmm-80) cc_final: 0.7411 (pmm-80) REVERT: C 328 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8933 (t) REVERT: C 406 GLU cc_start: 0.8396 (tt0) cc_final: 0.8178 (tt0) outliers start: 39 outliers final: 17 residues processed: 166 average time/residue: 0.4488 time to fit residues: 80.4044 Evaluate side-chains 151 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 177 CYS Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 399 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 HIS ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.199238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145216 restraints weight = 11135.362| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.22 r_work: 0.3503 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10419 Z= 0.146 Angle : 0.636 13.942 14199 Z= 0.321 Chirality : 0.045 0.202 1500 Planarity : 0.006 0.068 1821 Dihedral : 5.656 49.223 1372 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.70 % Favored : 91.75 % Rotamer: Outliers : 2.78 % Allowed : 29.93 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1272 helix: 0.98 (0.36), residues: 204 sheet: -0.68 (0.37), residues: 168 loop : -0.51 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 354 TYR 0.020 0.002 TYR A 385 PHE 0.015 0.001 PHE C 210 TRP 0.021 0.001 TRP A 236 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00339 (10401) covalent geometry : angle 0.63304 (14163) SS BOND : bond 0.00215 ( 18) SS BOND : angle 1.39348 ( 36) hydrogen bonds : bond 0.03658 ( 368) hydrogen bonds : angle 5.92235 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.256 Fit side-chains REVERT: A 63 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6593 (mtpp) REVERT: A 174 LYS cc_start: 0.8187 (pttt) cc_final: 0.7749 (pttm) REVERT: A 274 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7328 (t0) REVERT: A 346 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7418 (mmm) REVERT: A 412 ASP cc_start: 0.7621 (m-30) cc_final: 0.7335 (m-30) REVERT: B 58 MET cc_start: 0.7851 (mmt) cc_final: 0.7624 (mmt) REVERT: B 83 ARG cc_start: 0.8415 (mpt-90) cc_final: 0.7993 (mpt-90) REVERT: B 200 LYS cc_start: 0.7964 (mptt) cc_final: 0.7680 (mptt) REVERT: B 354 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7223 (ttm-80) REVERT: B 391 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5838 (tpt) REVERT: C 83 ARG cc_start: 0.7881 (pmm-80) cc_final: 0.7419 (pmm-80) REVERT: C 328 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8957 (t) REVERT: C 386 MET cc_start: 0.8108 (mmm) cc_final: 0.7741 (mmm) REVERT: C 406 GLU cc_start: 0.8415 (tt0) cc_final: 0.8201 (tt0) outliers start: 31 outliers final: 16 residues processed: 153 average time/residue: 0.4328 time to fit residues: 71.6712 Evaluate side-chains 149 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 177 CYS Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 399 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.197211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142707 restraints weight = 11123.411| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.22 r_work: 0.3476 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10419 Z= 0.180 Angle : 0.662 14.005 14199 Z= 0.336 Chirality : 0.046 0.204 1500 Planarity : 0.006 0.069 1821 Dihedral : 5.805 49.617 1372 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.47 % Favored : 91.98 % Rotamer: Outliers : 2.33 % Allowed : 30.47 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1272 helix: 0.81 (0.35), residues: 204 sheet: -0.68 (0.36), residues: 168 loop : -0.53 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 354 TYR 0.021 0.002 TYR A 385 PHE 0.016 0.001 PHE C 210 TRP 0.029 0.001 TRP A 236 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00419 (10401) covalent geometry : angle 0.65825 (14163) SS BOND : bond 0.00242 ( 18) SS BOND : angle 1.46917 ( 36) hydrogen bonds : bond 0.03836 ( 368) hydrogen bonds : angle 5.92908 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.364 Fit side-chains REVERT: A 63 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6586 (mtpp) REVERT: A 174 LYS cc_start: 0.8214 (pttt) cc_final: 0.7775 (pttm) REVERT: A 346 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7425 (mmm) REVERT: A 412 ASP cc_start: 0.7614 (m-30) cc_final: 0.7337 (m-30) REVERT: B 53 GLN cc_start: 0.8489 (mm110) cc_final: 0.8171 (mt0) REVERT: B 58 MET cc_start: 0.7844 (mmt) cc_final: 0.7631 (mmt) REVERT: B 83 ARG cc_start: 0.8438 (mpt-90) cc_final: 0.8031 (mpt-90) REVERT: B 200 LYS cc_start: 0.7968 (mptt) cc_final: 0.7650 (mptt) REVERT: B 354 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7168 (ttm-80) REVERT: B 391 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6133 (tpt) REVERT: C 78 ILE cc_start: 0.4187 (OUTLIER) cc_final: 0.3932 (tt) REVERT: C 83 ARG cc_start: 0.7903 (pmm-80) cc_final: 0.7470 (pmm-80) REVERT: C 328 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8979 (t) REVERT: C 386 MET cc_start: 0.8062 (mmm) cc_final: 0.7688 (mmm) REVERT: C 406 GLU cc_start: 0.8438 (tt0) cc_final: 0.8215 (tt0) outliers start: 26 outliers final: 18 residues processed: 150 average time/residue: 0.5547 time to fit residues: 89.5694 Evaluate side-chains 152 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 177 CYS Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 399 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.197839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143609 restraints weight = 11241.129| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.23 r_work: 0.3488 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10419 Z= 0.161 Angle : 0.649 14.363 14199 Z= 0.330 Chirality : 0.046 0.209 1500 Planarity : 0.006 0.069 1821 Dihedral : 5.788 49.825 1372 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.86 % Favored : 91.67 % Rotamer: Outliers : 2.42 % Allowed : 30.38 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1272 helix: 0.83 (0.35), residues: 204 sheet: -0.67 (0.36), residues: 168 loop : -0.53 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 354 TYR 0.020 0.002 TYR A 385 PHE 0.016 0.001 PHE C 210 TRP 0.028 0.001 TRP A 236 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00373 (10401) covalent geometry : angle 0.64605 (14163) SS BOND : bond 0.00235 ( 18) SS BOND : angle 1.38457 ( 36) hydrogen bonds : bond 0.03732 ( 368) hydrogen bonds : angle 5.89817 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3498.43 seconds wall clock time: 60 minutes 16.08 seconds (3616.08 seconds total)