Starting phenix.real_space_refine on Tue Aug 4 22:21:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8d_34543/08_2026/8h8d_34543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8d_34543/08_2026/8h8d_34543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h8d_34543/08_2026/8h8d_34543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8d_34543/08_2026/8h8d_34543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h8d_34543/08_2026/8h8d_34543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8d_34543/08_2026/8h8d_34543.map" } resolution = 4.26 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= -0.002 sd= 0.054 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 39 5.16 5 C 4587 2.51 5 N 1179 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7054 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2366 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 275} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2337 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain: "C" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2351 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Time building chain proxies: 1.76, per 1000 atoms: 0.25 Number of scatterers: 7054 At special positions: 0 Unit cell: (80.438, 80.438, 140.223, 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 39 16.00 O 1249 8.00 N 1179 7.00 C 4587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 151 " 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: 0.71 Conformation dependent library (CDL) restraints added in 504.1 milliseconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1652 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 34.5% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 56 through 99 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.655A pdb=" N PHE A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 304 through 343 Processing helix chain 'B' and resid 61 through 97 removed outlier: 3.689A pdb=" N MET B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.716A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 304 through 342 removed outlier: 3.789A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 69 through 99 removed outlier: 4.051A pdb=" N TYR C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 Processing helix chain 'C' and resid 217 through 229 removed outlier: 3.521A pdb=" N CYS C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 227 " --> pdb=" O GLN C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 344 removed outlier: 3.575A pdb=" N ALA C 310 " --> pdb=" O TRP C 306 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.944A pdb=" N GLN A 295 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 299 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS A 190 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU A 126 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.944A pdb=" N GLN A 295 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 299 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 261 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 155 removed outlier: 3.716A pdb=" N ILE A 172 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 119 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 201 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 108 removed outlier: 8.167A pdb=" N TYR B 293 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 246 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 295 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP B 299 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 154 through 159 removed outlier: 3.506A pdb=" N GLN B 154 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 156 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 170 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 117 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 202 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 131 removed outlier: 3.640A pdb=" N HIS B 190 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLN B 188 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 129 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE B 186 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE B 238 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B 284 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 108 removed outlier: 14.129A pdb=" N TYR C 293 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N MET C 244 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N GLN C 295 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU C 246 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE C 297 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS C 248 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 240 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 188 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 128 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N HIS C 190 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU C 126 " --> pdb=" O HIS C 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 108 removed outlier: 14.129A pdb=" N TYR C 293 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N MET C 244 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N GLN C 295 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU C 246 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE C 297 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS C 248 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 243 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 117 through 120 removed outlier: 4.371A pdb=" N ASP C 202 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 159 374 hydrogen bonds defined for protein. 1062 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: 1.16 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1833 1.33 - 1.45: 1377 1.45 - 1.57: 3970 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 7243 Sorted by residual: bond pdb=" CE1 HIS B 340 " pdb=" NE2 HIS B 340 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.60e+01 bond pdb=" N ILE B 300 " pdb=" CA ILE B 300 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N VAL B 330 " pdb=" CA VAL B 330 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.87e+00 bond pdb=" N ILE B 301 " pdb=" CA ILE B 301 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.72e+00 bond pdb=" N ILE A 301 " pdb=" CA ILE A 301 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.71e+00 ... (remaining 7238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 9436 2.16 - 4.31: 310 4.31 - 6.47: 32 6.47 - 8.62: 9 8.62 - 10.78: 6 Bond angle restraints: 9793 Sorted by residual: angle pdb=" C ILE A 159 " pdb=" N ASP A 160 " pdb=" CA ASP A 160 " ideal model delta sigma weight residual 120.49 131.27 -10.78 1.42e+00 4.96e-01 5.76e+01 angle pdb=" N LYS A 321 " pdb=" CA LYS A 321 " pdb=" C LYS A 321 " ideal model delta sigma weight residual 111.36 105.92 5.44 1.09e+00 8.42e-01 2.49e+01 angle pdb=" CA ARG B 182 " pdb=" CB ARG B 182 " pdb=" CG ARG B 182 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 angle pdb=" N THR B 302 " pdb=" CA THR B 302 " pdb=" C THR B 302 " ideal model delta sigma weight residual 111.28 115.55 -4.27 1.09e+00 8.42e-01 1.53e+01 angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 109.07 115.28 -6.21 1.61e+00 3.86e-01 1.49e+01 ... (remaining 9788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3622 17.90 - 35.81: 530 35.81 - 53.71: 137 53.71 - 71.62: 30 71.62 - 89.52: 13 Dihedral angle restraints: 4332 sinusoidal: 1795 harmonic: 2537 Sorted by residual: dihedral pdb=" CD ARG B 337 " pdb=" NE ARG B 337 " pdb=" CZ ARG B 337 " pdb=" NH1 ARG B 337 " ideal model delta sinusoidal sigma weight residual 0.00 -78.44 78.44 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS B 129 " pdb=" SG CYS B 129 " pdb=" SG CYS B 151 " pdb=" CB CYS B 151 " ideal model delta sinusoidal sigma weight residual 93.00 41.68 51.32 1 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" CD ARG B 339 " pdb=" NE ARG B 339 " pdb=" CZ ARG B 339 " pdb=" NH1 ARG B 339 " ideal model delta sinusoidal sigma weight residual 0.00 -48.39 48.39 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 765 0.044 - 0.089: 192 0.089 - 0.133: 76 0.133 - 0.178: 14 0.178 - 0.222: 17 Chirality restraints: 1064 Sorted by residual: chirality pdb=" CA VAL B 315 " pdb=" N VAL B 315 " pdb=" C VAL B 315 " pdb=" CB VAL B 315 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A 318 " pdb=" N VAL A 318 " pdb=" C VAL A 318 " pdb=" CB VAL A 318 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL B 318 " pdb=" CA VAL B 318 " pdb=" CG1 VAL B 318 " pdb=" CG2 VAL B 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1061 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 337 " 1.083 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG B 337 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG B 337 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 337 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 337 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 339 " 0.820 9.50e-02 1.11e+02 3.67e-01 8.20e+01 pdb=" NE ARG B 339 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 339 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 339 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 339 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 197 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" CG ASP A 197 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP A 197 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 197 " 0.017 2.00e-02 2.50e+03 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 271 2.70 - 3.25: 7641 3.25 - 3.80: 11911 3.80 - 4.35: 14178 4.35 - 4.90: 21981 Nonbonded interactions: 55982 Sorted by model distance: nonbonded pdb=" OD1 ASP A 197 " pdb=" N PHE A 198 " model vdw 2.155 3.120 nonbonded pdb=" O ARG B 181 " pdb=" NH1 ARG B 181 " model vdw 2.192 3.120 nonbonded pdb=" O ALA B 211 " pdb=" OG SER B 215 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR C 302 " pdb=" OD1 ASN C 304 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASN B 268 " pdb=" N PHE B 269 " model vdw 2.232 3.120 ... (remaining 55977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 61 through 342) selection = (chain 'B' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'C' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.710 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 0.040 7246 Z= 0.282 Angle : 0.868 10.779 9799 Z= 0.539 Chirality : 0.053 0.222 1064 Planarity : 0.018 0.485 1229 Dihedral : 18.367 89.523 2671 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.97 % Allowed : 30.45 % Favored : 64.59 % 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: -0.02 (0.30), residues: 850 helix: 1.85 (0.30), residues: 288 sheet: -0.45 (0.31), residues: 289 loop : -1.49 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.014 0.001 TYR A 120 PHE 0.022 0.001 PHE A 320 TRP 0.035 0.002 TRP C 133 HIS 0.007 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.28 ( 7243) covalent geometry : angle 0.86688 / 0.54 ( 9793) SS BOND : bond 0.00138 / 0.06 ( 3) SS BOND : angle 1.81238 / 0.99 ( 6) hydrogen bonds : bond 0.20476 / 13.79 ( 357) hydrogen bonds : angle 7.40718 / 5.09 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 MET cc_start: 0.8608 (ptm) cc_final: 0.8395 (ppp) REVERT: B 325 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9100 (p90) REVERT: B 338 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.4702 (mmm160) REVERT: B 340 HIS cc_start: -0.2636 (OUTLIER) cc_final: -0.2867 (t-90) REVERT: C 154 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8426 (tm-30) outliers start: 39 outliers final: 17 residues processed: 130 average time/residue: 0.0886 time to fit residues: 15.7284 Evaluate side-chains 118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN C 174 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.091860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.065284 restraints weight = 26872.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066983 restraints weight = 16461.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.068046 restraints weight = 12090.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.068786 restraints weight = 9942.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069114 restraints weight = 8791.073| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7246 Z= 0.181 Angle : 0.658 8.349 9799 Z= 0.347 Chirality : 0.044 0.186 1064 Planarity : 0.005 0.072 1229 Dihedral : 4.881 20.041 928 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -0.25 (0.30), residues: 850 helix: 1.34 (0.29), residues: 293 sheet: -0.45 (0.30), residues: 295 loop : -1.44 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 337 TYR 0.019 0.002 TYR B 158 PHE 0.025 0.002 PHE A 320 TRP 0.013 0.002 TRP B 232 HIS 0.006 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 7243) covalent geometry : angle 0.65680 / 0.35 ( 9793) SS BOND : bond 0.01418 / 0.53 ( 3) SS BOND : angle 1.99998 / 1.15 ( 6) hydrogen bonds : bond 0.04821 / 3.01 ( 357) hydrogen bonds : angle 5.44813 / 3.82 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 MET cc_start: 0.8724 (ptm) cc_final: 0.8470 (ppp) REVERT: B 158 TYR cc_start: 0.8045 (m-10) cc_final: 0.7778 (m-10) REVERT: B 333 MET cc_start: 0.6792 (tpp) cc_final: 0.6307 (tmm) REVERT: C 79 MET cc_start: 0.8809 (mmp) cc_final: 0.8517 (mmm) REVERT: C 169 HIS cc_start: 0.7707 (t-170) cc_final: 0.7507 (t-90) REVERT: C 222 MET cc_start: 0.8567 (ppp) cc_final: 0.8333 (ppp) REVERT: C 233 LYS cc_start: 0.9068 (tptt) cc_final: 0.8796 (tptt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0638 time to fit residues: 12.3160 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 43 optimal weight: 0.0570 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.093114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070622 restraints weight = 26695.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070479 restraints weight = 18525.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.071025 restraints weight = 15931.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.071354 restraints weight = 12909.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071614 restraints weight = 11808.002| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7246 Z= 0.120 Angle : 0.612 7.501 9799 Z= 0.314 Chirality : 0.042 0.147 1064 Planarity : 0.004 0.074 1229 Dihedral : 4.675 20.814 928 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: -0.23 (0.30), residues: 850 helix: 1.26 (0.29), residues: 293 sheet: -0.33 (0.30), residues: 292 loop : -1.43 (0.43), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.015 0.001 TYR C 203 PHE 0.026 0.001 PHE C 325 TRP 0.013 0.001 TRP C 241 HIS 0.005 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7243) covalent geometry : angle 0.61171 / 0.31 ( 9793) SS BOND : bond 0.00228 / 0.09 ( 3) SS BOND : angle 0.81986 / 0.45 ( 6) hydrogen bonds : bond 0.04066 / 2.59 ( 357) hydrogen bonds : angle 4.92631 / 3.47 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9118 (tmm) cc_final: 0.8871 (tmm) REVERT: B 222 MET cc_start: 0.7891 (tmm) cc_final: 0.7617 (tmm) REVERT: B 309 ILE cc_start: 0.9584 (tp) cc_final: 0.9335 (pt) REVERT: B 333 MET cc_start: 0.6961 (tpp) cc_final: 0.6421 (tmm) REVERT: C 79 MET cc_start: 0.8907 (mmp) cc_final: 0.8465 (mmm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0638 time to fit residues: 10.9610 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.090970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067549 restraints weight = 27229.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.067969 restraints weight = 20138.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068322 restraints weight = 14625.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.068628 restraints weight = 12980.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.068992 restraints weight = 11785.853| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7246 Z= 0.158 Angle : 0.601 9.470 9799 Z= 0.311 Chirality : 0.041 0.158 1064 Planarity : 0.005 0.126 1229 Dihedral : 4.703 19.596 928 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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: -0.14 (0.30), residues: 850 helix: 1.42 (0.28), residues: 290 sheet: -0.22 (0.31), residues: 286 loop : -1.53 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 181 TYR 0.019 0.001 TYR C 203 PHE 0.019 0.002 PHE A 320 TRP 0.022 0.002 TRP B 232 HIS 0.005 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 7243) covalent geometry : angle 0.60069 / 0.31 ( 9793) SS BOND : bond 0.00160 / 0.07 ( 3) SS BOND : angle 1.38156 / 0.80 ( 6) hydrogen bonds : bond 0.03685 / 2.38 ( 357) hydrogen bonds : angle 4.77006 / 3.36 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9136 (tmm) cc_final: 0.8870 (tmm) REVERT: B 222 MET cc_start: 0.7906 (tmm) cc_final: 0.7620 (tmm) REVERT: B 309 ILE cc_start: 0.9504 (tp) cc_final: 0.9264 (pt) REVERT: B 333 MET cc_start: 0.6980 (tpp) cc_final: 0.6549 (tmm) REVERT: C 79 MET cc_start: 0.8899 (mmp) cc_final: 0.8434 (mmm) REVERT: C 222 MET cc_start: 0.8473 (ppp) cc_final: 0.8256 (ppp) REVERT: C 321 LYS cc_start: 0.9581 (tptt) cc_final: 0.9219 (tppt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0636 time to fit residues: 10.3970 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 0.0170 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS B 295 GLN C 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.090429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067152 restraints weight = 27250.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.067754 restraints weight = 20347.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.068085 restraints weight = 14338.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.068423 restraints weight = 12899.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068677 restraints weight = 11671.666| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7246 Z= 0.160 Angle : 0.611 7.695 9799 Z= 0.317 Chirality : 0.042 0.157 1064 Planarity : 0.005 0.127 1229 Dihedral : 4.745 20.010 928 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.30), residues: 850 helix: 1.46 (0.28), residues: 290 sheet: -0.19 (0.31), residues: 292 loop : -1.51 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 181 TYR 0.021 0.001 TYR C 203 PHE 0.017 0.002 PHE C 325 TRP 0.024 0.002 TRP B 232 HIS 0.014 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7243) covalent geometry : angle 0.61047 / 0.32 ( 9793) SS BOND : bond 0.00141 / 0.06 ( 3) SS BOND : angle 1.39891 / 0.82 ( 6) hydrogen bonds : bond 0.03613 / 2.38 ( 357) hydrogen bonds : angle 4.70912 / 3.33 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9147 (tmm) cc_final: 0.8869 (tmm) REVERT: B 222 MET cc_start: 0.7967 (tmm) cc_final: 0.7707 (tmm) REVERT: B 333 MET cc_start: 0.7038 (tpp) cc_final: 0.6608 (tmm) REVERT: C 79 MET cc_start: 0.8879 (mmp) cc_final: 0.8412 (mmm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0603 time to fit residues: 8.9883 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 79 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.090793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064154 restraints weight = 27296.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065801 restraints weight = 16802.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.066910 restraints weight = 12368.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067618 restraints weight = 10147.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.068152 restraints weight = 8950.700| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7246 Z= 0.135 Angle : 0.588 7.449 9799 Z= 0.303 Chirality : 0.041 0.165 1064 Planarity : 0.005 0.110 1229 Dihedral : 4.600 20.221 928 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.00 (0.30), residues: 850 helix: 1.59 (0.29), residues: 287 sheet: -0.19 (0.31), residues: 291 loop : -1.42 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 181 TYR 0.018 0.001 TYR C 203 PHE 0.021 0.001 PHE B 316 TRP 0.020 0.001 TRP B 232 HIS 0.012 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7243) covalent geometry : angle 0.58728 / 0.30 ( 9793) SS BOND : bond 0.00131 / 0.06 ( 3) SS BOND : angle 1.11440 / 0.65 ( 6) hydrogen bonds : bond 0.03386 / 2.24 ( 357) hydrogen bonds : angle 4.57020 / 3.23 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9155 (tmm) cc_final: 0.8872 (tmm) REVERT: A 316 PHE cc_start: 0.9353 (m-10) cc_final: 0.9138 (m-80) REVERT: B 222 MET cc_start: 0.7846 (tmm) cc_final: 0.7594 (tmm) REVERT: B 268 ASN cc_start: 0.8919 (t0) cc_final: 0.8605 (t0) REVERT: B 333 MET cc_start: 0.6849 (tpp) cc_final: 0.6462 (tmm) REVERT: C 79 MET cc_start: 0.8869 (mmp) cc_final: 0.8383 (mmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0501 time to fit residues: 7.6047 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 8 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.2893 > 50:) chunk 75 optimal weight: 0.0000 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.0070 chunk 73 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 overall best weight: 0.6604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.092058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065675 restraints weight = 26839.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.067394 restraints weight = 16384.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.068470 restraints weight = 11937.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069276 restraints weight = 9780.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.069739 restraints weight = 8551.487| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7246 Z= 0.112 Angle : 0.604 8.416 9799 Z= 0.303 Chirality : 0.043 0.229 1064 Planarity : 0.004 0.098 1229 Dihedral : 4.473 20.274 928 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 0.06 (0.30), residues: 850 helix: 1.51 (0.29), residues: 291 sheet: -0.09 (0.31), residues: 287 loop : -1.34 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 181 TYR 0.017 0.001 TYR C 203 PHE 0.013 0.001 PHE C 234 TRP 0.019 0.002 TRP C 289 HIS 0.010 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 7243) covalent geometry : angle 0.60291 / 0.30 ( 9793) SS BOND : bond 0.00121 / 0.05 ( 3) SS BOND : angle 1.56694 / 0.92 ( 6) hydrogen bonds : bond 0.03198 / 2.12 ( 357) hydrogen bonds : angle 4.37958 / 3.11 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.8976 (t0) cc_final: 0.8605 (t0) REVERT: B 333 MET cc_start: 0.6861 (tpp) cc_final: 0.6465 (tmm) REVERT: C 79 MET cc_start: 0.8869 (mmp) cc_final: 0.8414 (mmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0537 time to fit residues: 8.5736 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 75 optimal weight: 0.0010 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.091577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069206 restraints weight = 27221.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.067989 restraints weight = 20687.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069045 restraints weight = 15358.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069126 restraints weight = 12069.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.069300 restraints weight = 11248.785| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7246 Z= 0.123 Angle : 0.627 9.201 9799 Z= 0.315 Chirality : 0.043 0.263 1064 Planarity : 0.004 0.093 1229 Dihedral : 4.478 20.319 928 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -0.02 (0.30), residues: 850 helix: 1.45 (0.29), residues: 290 sheet: -0.14 (0.31), residues: 284 loop : -1.37 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 181 TYR 0.028 0.001 TYR B 75 PHE 0.046 0.001 PHE A 316 TRP 0.024 0.002 TRP B 232 HIS 0.010 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7243) covalent geometry : angle 0.62608 / 0.31 ( 9793) SS BOND : bond 0.00210 / 0.10 ( 3) SS BOND : angle 1.47109 / 0.85 ( 6) hydrogen bonds : bond 0.03238 / 2.16 ( 357) hydrogen bonds : angle 4.41545 / 3.15 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 MET cc_start: 0.8294 (tmm) cc_final: 0.7897 (tmm) REVERT: B 333 MET cc_start: 0.6959 (tpp) cc_final: 0.6541 (tmm) REVERT: C 79 MET cc_start: 0.8867 (mmp) cc_final: 0.8374 (mmm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0519 time to fit residues: 8.1477 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.090070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063505 restraints weight = 27381.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065114 restraints weight = 16856.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.066227 restraints weight = 12452.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.066940 restraints weight = 10245.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067291 restraints weight = 9025.476| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7246 Z= 0.154 Angle : 0.637 8.027 9799 Z= 0.323 Chirality : 0.042 0.244 1064 Planarity : 0.005 0.104 1229 Dihedral : 4.630 20.171 928 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.08 (0.30), residues: 850 helix: 1.45 (0.29), residues: 290 sheet: -0.21 (0.31), residues: 293 loop : -1.46 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 181 TYR 0.022 0.001 TYR B 75 PHE 0.033 0.002 PHE A 316 TRP 0.027 0.002 TRP B 232 HIS 0.010 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7243) covalent geometry : angle 0.63575 / 0.32 ( 9793) SS BOND : bond 0.00152 / 0.07 ( 3) SS BOND : angle 1.41434 / 0.82 ( 6) hydrogen bonds : bond 0.03328 / 2.21 ( 357) hydrogen bonds : angle 4.49790 / 3.21 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 PHE cc_start: 0.9418 (m-80) cc_final: 0.9192 (m-80) REVERT: B 232 TRP cc_start: 0.7938 (m-10) cc_final: 0.7553 (m-10) REVERT: B 268 ASN cc_start: 0.8888 (t0) cc_final: 0.8601 (t0) REVERT: B 333 MET cc_start: 0.6887 (tpp) cc_final: 0.6501 (tmm) REVERT: C 79 MET cc_start: 0.8872 (mmp) cc_final: 0.8390 (mmm) REVERT: C 321 LYS cc_start: 0.9673 (tptp) cc_final: 0.9449 (tptp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0524 time to fit residues: 7.5093 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.0000 chunk 54 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.090489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064225 restraints weight = 27282.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065848 restraints weight = 16872.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.066977 restraints weight = 12457.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.067500 restraints weight = 10225.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068120 restraints weight = 9174.320| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7246 Z= 0.137 Angle : 0.632 8.484 9799 Z= 0.317 Chirality : 0.042 0.246 1064 Planarity : 0.005 0.102 1229 Dihedral : 4.649 22.245 928 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.02 (0.30), residues: 850 helix: 1.49 (0.29), residues: 290 sheet: -0.20 (0.30), residues: 299 loop : -1.40 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 181 TYR 0.019 0.001 TYR B 75 PHE 0.031 0.001 PHE A 316 TRP 0.023 0.002 TRP B 232 HIS 0.011 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7243) covalent geometry : angle 0.63140 / 0.32 ( 9793) SS BOND : bond 0.00145 / 0.06 ( 3) SS BOND : angle 1.37833 / 0.79 ( 6) hydrogen bonds : bond 0.03269 / 2.16 ( 357) hydrogen bonds : angle 4.43739 / 3.17 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 PHE cc_start: 0.9426 (m-80) cc_final: 0.9203 (m-80) REVERT: B 222 MET cc_start: 0.7972 (tmm) cc_final: 0.7762 (tmm) REVERT: B 232 TRP cc_start: 0.7897 (m-10) cc_final: 0.7527 (m-10) REVERT: B 268 ASN cc_start: 0.8940 (t0) cc_final: 0.8683 (t0) REVERT: B 333 MET cc_start: 0.6935 (tpp) cc_final: 0.6499 (tmm) REVERT: C 79 MET cc_start: 0.8873 (mmp) cc_final: 0.8394 (mmm) REVERT: C 321 LYS cc_start: 0.9666 (tptp) cc_final: 0.9439 (tptp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0532 time to fit residues: 7.7158 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066208 restraints weight = 27225.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.066736 restraints weight = 20912.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067056 restraints weight = 14728.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.067502 restraints weight = 13302.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.067681 restraints weight = 11946.449| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7246 Z= 0.148 Angle : 0.641 8.440 9799 Z= 0.325 Chirality : 0.042 0.244 1064 Planarity : 0.005 0.104 1229 Dihedral : 4.679 24.663 928 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.06 (0.29), residues: 850 helix: 1.47 (0.29), residues: 290 sheet: -0.22 (0.30), residues: 298 loop : -1.45 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 181 TYR 0.017 0.001 TYR B 75 PHE 0.031 0.001 PHE A 316 TRP 0.024 0.002 TRP B 232 HIS 0.010 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 7243) covalent geometry : angle 0.64048 / 0.32 ( 9793) SS BOND : bond 0.00171 / 0.07 ( 3) SS BOND : angle 1.39463 / 0.80 ( 6) hydrogen bonds : bond 0.03409 / 2.22 ( 357) hydrogen bonds : angle 4.48353 / 3.21 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1175.90 seconds wall clock time: 20 minutes 57.55 seconds (1257.55 seconds total)