Starting phenix.real_space_refine on Thu Jul 2 20:18:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjr_39347/07_2026/8yjr_39347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjr_39347/07_2026/8yjr_39347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yjr_39347/07_2026/8yjr_39347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjr_39347/07_2026/8yjr_39347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yjr_39347/07_2026/8yjr_39347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjr_39347/07_2026/8yjr_39347.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 263 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 61 5.16 5 C 6072 2.51 5 N 1671 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9962 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1963 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "D" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2774 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 228 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 9962 At special positions: 0 Unit cell: (106.24, 102.92, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 65 15.00 O 2093 8.00 N 1671 7.00 C 6072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " 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: 0.95 Conformation dependent library (CDL) restraints added in 281.4 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 29.3% alpha, 24.9% beta 10 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.457A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.972A pdb=" N TYR D 26 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.737A pdb=" N ILE D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 46 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.682A pdb=" N MET D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 116 removed outlier: 4.009A pdb=" N ALA D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 134 through 148 removed outlier: 3.569A pdb=" N ASN D 138 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 230 removed outlier: 3.678A pdb=" N ASP D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 253 Processing helix chain 'D' and resid 255 through 262 removed outlier: 3.570A pdb=" N ILE D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 333 removed outlier: 3.632A pdb=" N GLN D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.566A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.617A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 196 " --> pdb=" O LYS B 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 208 removed outlier: 5.513A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 167 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 179 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 71 removed outlier: 6.783A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 123 through 127 removed outlier: 5.825A pdb=" N GLY C 127 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL D 346 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 208 removed outlier: 5.088A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 167 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.254A pdb=" N ALA D 175 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS D 30 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA D 176 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 32 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 31 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 84 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE D 33 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.521A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 251 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.23 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: 2562 1.33 - 1.45: 2028 1.45 - 1.58: 5430 1.58 - 1.70: 126 1.70 - 1.82: 98 Bond restraints: 10244 Sorted by residual: bond pdb=" C3' DT E 0 " pdb=" O3' DT E 0 " ideal model delta sigma weight residual 1.435 1.492 -0.057 1.30e-02 5.92e+03 1.93e+01 bond pdb=" C1' DT J 20 " pdb=" N1 DT J 20 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.79e+01 bond pdb=" C3' DA E 14 " pdb=" O3' DA E 14 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" C3' DA J 15 " pdb=" O3' DA J 15 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" C3' DA E 20 " pdb=" C2' DA E 20 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 10239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13806 2.93 - 5.86: 251 5.86 - 8.79: 32 8.79 - 11.72: 8 11.72 - 14.65: 1 Bond angle restraints: 14098 Sorted by residual: angle pdb=" C ALA A 242 " pdb=" N ASP A 243 " pdb=" CA ASP A 243 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C ALA B 242 " pdb=" N ASP B 243 " pdb=" CA ASP B 243 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N THR B 219 " pdb=" CA THR B 219 " pdb=" C THR B 219 " ideal model delta sigma weight residual 109.81 120.02 -10.21 2.21e+00 2.05e-01 2.14e+01 angle pdb=" C ALA C 231 " pdb=" N ASP C 232 " pdb=" CA ASP C 232 " ideal model delta sigma weight residual 121.54 129.93 -8.39 1.91e+00 2.74e-01 1.93e+01 angle pdb=" N3 DT J 11 " pdb=" C4 DT J 11 " pdb=" O4 DT J 11 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 14093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 5762 35.17 - 70.34: 408 70.34 - 105.51: 16 105.51 - 140.68: 1 140.68 - 175.85: 2 Dihedral angle restraints: 6189 sinusoidal: 2949 harmonic: 3240 Sorted by residual: dihedral pdb=" C4' DT E 0 " pdb=" C3' DT E 0 " pdb=" O3' DT E 0 " pdb=" P DT E 1 " ideal model delta sinusoidal sigma weight residual -140.00 35.85 -175.85 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA THR B 216 " pdb=" C THR B 216 " pdb=" N LYS B 217 " pdb=" CA LYS B 217 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C4' DA E 14 " pdb=" C3' DA E 14 " pdb=" O3' DA E 14 " pdb=" P DA E 15 " ideal model delta sinusoidal sigma weight residual -140.00 4.42 -144.42 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 6186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1201 0.054 - 0.108: 316 0.108 - 0.162: 85 0.162 - 0.216: 16 0.216 - 0.270: 5 Chirality restraints: 1623 Sorted by residual: chirality pdb=" CB ILE A 128 " pdb=" CA ILE A 128 " pdb=" CG1 ILE A 128 " pdb=" CG2 ILE A 128 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" P DA E 15 " pdb=" OP1 DA E 15 " pdb=" OP2 DA E 15 " pdb=" O5' DA E 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.60 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL A 45 " pdb=" CA VAL A 45 " pdb=" CG1 VAL A 45 " pdb=" CG2 VAL A 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1620 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 219 " 0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO B 220 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.052 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO A 220 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 233 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO B 234 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.037 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2889 2.84 - 3.36: 8152 3.36 - 3.87: 17979 3.87 - 4.39: 19717 4.39 - 4.90: 33111 Nonbonded interactions: 81848 Sorted by model distance: nonbonded pdb=" O VAL D 123 " pdb=" OG1 THR D 127 " model vdw 2.330 3.040 nonbonded pdb=" OG SER A 43 " pdb=" OH TYR A 211 " model vdw 2.372 3.040 nonbonded pdb=" OG SER C 43 " pdb=" OH TYR C 211 " model vdw 2.375 3.040 nonbonded pdb=" OD2 ASP C 41 " pdb=" OG SER C 43 " model vdw 2.376 3.040 nonbonded pdb=" OG SER B 141 " pdb=" O SER B 222 " model vdw 2.390 3.040 ... (remaining 81843 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' selection = chain 'B' selection = (chain 'C' and resid 2 through 254) } 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.130 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.005 0.059 10247 Z= 0.352 Angle : 0.986 14.649 14104 Z= 0.622 Chirality : 0.056 0.270 1623 Planarity : 0.007 0.085 1593 Dihedral : 20.532 175.855 4078 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -3.40 (0.21), residues: 1105 helix: -2.95 (0.19), residues: 314 sheet: -1.36 (0.30), residues: 290 loop : -2.22 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 146 TYR 0.024 0.003 TYR D 69 PHE 0.028 0.002 PHE D 283 TRP 0.007 0.001 TRP B 28 HIS 0.005 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.35 (10244) covalent geometry : angle 0.98605 / 0.62 (14098) SS BOND : bond 0.00114 / 0.06 ( 3) SS BOND : angle 0.63377 / 0.59 ( 6) hydrogen bonds : bond 0.20670 / 13.59 ( 445) hydrogen bonds : angle 9.85319 / 6.63 ( 1234) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 MET cc_start: 0.6419 (tpt) cc_final: 0.5938 (ppp) REVERT: D 325 VAL cc_start: 0.8445 (t) cc_final: 0.7941 (m) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0902 time to fit residues: 19.0561 Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN B 131 GLN D 77 ASN D 273 ASN A 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.131353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.100986 restraints weight = 17110.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104311 restraints weight = 12921.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104570 restraints weight = 7828.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.104900 restraints weight = 7922.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106875 restraints weight = 7022.599| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10247 Z= 0.191 Angle : 0.673 7.528 14104 Z= 0.372 Chirality : 0.048 0.201 1623 Planarity : 0.005 0.051 1593 Dihedral : 21.958 168.505 1944 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.93 % Allowed : 9.83 % Favored : 89.23 % 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: -2.51 (0.22), residues: 1105 helix: -1.43 (0.24), residues: 332 sheet: -1.34 (0.28), residues: 319 loop : -1.91 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 192 TYR 0.020 0.002 TYR B 133 PHE 0.019 0.002 PHE D 126 TRP 0.006 0.001 TRP C 28 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (10244) covalent geometry : angle 0.67253 / 0.37 (14098) SS BOND : bond 0.00156 / 0.08 ( 3) SS BOND : angle 1.41475 / 0.85 ( 6) hydrogen bonds : bond 0.04862 / 3.21 ( 445) hydrogen bonds : angle 6.98458 / 4.76 ( 1234) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: D 37 MET cc_start: 0.7836 (mmm) cc_final: 0.7617 (mmt) REVERT: D 65 MET cc_start: 0.6800 (tpt) cc_final: 0.6373 (ppp) outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.0846 time to fit residues: 14.3014 Evaluate side-chains 97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 0.0050 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN D 273 ASN A 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.130431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.100271 restraints weight = 17192.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103478 restraints weight = 12329.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.104348 restraints weight = 7510.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.104610 restraints weight = 6847.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.104880 restraints weight = 6483.668| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10247 Z= 0.149 Angle : 0.592 6.938 14104 Z= 0.328 Chirality : 0.046 0.276 1623 Planarity : 0.004 0.049 1593 Dihedral : 21.975 169.737 1944 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.04 % Allowed : 12.53 % Favored : 86.44 % 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: -1.88 (0.23), residues: 1105 helix: -0.47 (0.27), residues: 326 sheet: -1.22 (0.27), residues: 335 loop : -1.70 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.014 0.001 TYR A 211 PHE 0.014 0.001 PHE D 126 TRP 0.004 0.001 TRP A 28 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (10244) covalent geometry : angle 0.59157 / 0.33 (14098) SS BOND : bond 0.00328 / 0.17 ( 3) SS BOND : angle 1.00789 / 0.60 ( 6) hydrogen bonds : bond 0.04025 / 2.66 ( 445) hydrogen bonds : angle 6.39290 / 4.36 ( 1234) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: B 199 MET cc_start: 0.8155 (tmm) cc_final: 0.7484 (tpp) REVERT: D 37 MET cc_start: 0.7852 (mmm) cc_final: 0.7641 (mmt) REVERT: D 65 MET cc_start: 0.6852 (tpt) cc_final: 0.6530 (ppp) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 0.0709 time to fit residues: 11.5386 Evaluate side-chains 95 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.129915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.099547 restraints weight = 17278.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.102845 restraints weight = 12414.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.103627 restraints weight = 7575.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.103810 restraints weight = 6934.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.104410 restraints weight = 6562.190| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10247 Z= 0.145 Angle : 0.580 9.451 14104 Z= 0.316 Chirality : 0.045 0.233 1623 Planarity : 0.004 0.042 1593 Dihedral : 21.993 170.022 1944 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.35 % Allowed : 14.08 % Favored : 84.58 % 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: -1.56 (0.24), residues: 1105 helix: 0.02 (0.28), residues: 328 sheet: -1.20 (0.27), residues: 343 loop : -1.57 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 146 TYR 0.018 0.002 TYR D 152 PHE 0.019 0.001 PHE D 68 TRP 0.004 0.001 TRP A 28 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (10244) covalent geometry : angle 0.57970 / 0.32 (14098) SS BOND : bond 0.00232 / 0.12 ( 3) SS BOND : angle 0.62457 / 0.38 ( 6) hydrogen bonds : bond 0.03577 / 2.36 ( 445) hydrogen bonds : angle 6.03612 / 4.10 ( 1234) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 199 MET cc_start: 0.8130 (tmm) cc_final: 0.7777 (tmm) REVERT: D 37 MET cc_start: 0.7831 (mmm) cc_final: 0.7473 (mmt) REVERT: D 65 MET cc_start: 0.7014 (tpt) cc_final: 0.6642 (ppp) REVERT: D 110 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7585 (mp10) outliers start: 13 outliers final: 6 residues processed: 108 average time/residue: 0.0887 time to fit residues: 14.3295 Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098911 restraints weight = 17118.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102197 restraints weight = 12262.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102976 restraints weight = 7564.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.103247 restraints weight = 6865.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103510 restraints weight = 6541.899| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10247 Z= 0.142 Angle : 0.568 8.118 14104 Z= 0.311 Chirality : 0.044 0.247 1623 Planarity : 0.003 0.041 1593 Dihedral : 21.999 170.749 1944 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.45 % Allowed : 15.22 % Favored : 83.33 % 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: -1.37 (0.24), residues: 1105 helix: 0.30 (0.29), residues: 328 sheet: -1.27 (0.26), residues: 357 loop : -1.37 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 73 TYR 0.016 0.001 TYR B 249 PHE 0.012 0.001 PHE D 126 TRP 0.004 0.001 TRP A 28 HIS 0.001 0.000 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10244) covalent geometry : angle 0.56846 / 0.31 (14098) SS BOND : bond 0.00232 / 0.12 ( 3) SS BOND : angle 0.63587 / 0.40 ( 6) hydrogen bonds : bond 0.03469 / 2.26 ( 445) hydrogen bonds : angle 5.87732 / 3.99 ( 1234) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: B 199 MET cc_start: 0.8026 (tmm) cc_final: 0.7712 (tmm) REVERT: D 65 MET cc_start: 0.6999 (tpt) cc_final: 0.6683 (ppp) outliers start: 14 outliers final: 7 residues processed: 104 average time/residue: 0.0860 time to fit residues: 13.5822 Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.129472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098894 restraints weight = 17118.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.102268 restraints weight = 12362.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.102987 restraints weight = 7582.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.103248 restraints weight = 6923.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103541 restraints weight = 6577.346| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10247 Z= 0.135 Angle : 0.564 8.579 14104 Z= 0.307 Chirality : 0.044 0.253 1623 Planarity : 0.003 0.041 1593 Dihedral : 21.961 171.316 1944 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.55 % Allowed : 15.63 % Favored : 82.82 % 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: -1.23 (0.24), residues: 1105 helix: 0.47 (0.29), residues: 328 sheet: -1.21 (0.26), residues: 354 loop : -1.33 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 146 TYR 0.017 0.001 TYR D 152 PHE 0.014 0.001 PHE D 126 TRP 0.004 0.001 TRP A 28 HIS 0.001 0.000 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10244) covalent geometry : angle 0.56376 / 0.31 (14098) SS BOND : bond 0.00305 / 0.15 ( 3) SS BOND : angle 0.50769 / 0.33 ( 6) hydrogen bonds : bond 0.03315 / 2.17 ( 445) hydrogen bonds : angle 5.75347 / 3.90 ( 1234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: B 116 MET cc_start: 0.6958 (mtp) cc_final: 0.6687 (mtp) REVERT: D 65 MET cc_start: 0.7004 (tpt) cc_final: 0.6717 (ppp) REVERT: D 75 MET cc_start: 0.8607 (mmm) cc_final: 0.8396 (mmm) outliers start: 15 outliers final: 7 residues processed: 107 average time/residue: 0.0872 time to fit residues: 14.1773 Evaluate side-chains 95 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.128814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.098215 restraints weight = 17182.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101550 restraints weight = 12352.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102380 restraints weight = 7594.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102565 restraints weight = 6830.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103143 restraints weight = 6514.446| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10247 Z= 0.148 Angle : 0.581 8.559 14104 Z= 0.314 Chirality : 0.045 0.262 1623 Planarity : 0.003 0.039 1593 Dihedral : 21.929 171.651 1944 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.45 % Allowed : 16.25 % Favored : 82.30 % 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: -1.11 (0.25), residues: 1105 helix: 0.59 (0.29), residues: 328 sheet: -1.21 (0.26), residues: 357 loop : -1.21 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.015 0.001 TYR D 40 PHE 0.027 0.001 PHE D 68 TRP 0.004 0.001 TRP A 28 HIS 0.002 0.000 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (10244) covalent geometry : angle 0.58140 / 0.31 (14098) SS BOND : bond 0.00161 / 0.08 ( 3) SS BOND : angle 0.51301 / 0.35 ( 6) hydrogen bonds : bond 0.03329 / 2.17 ( 445) hydrogen bonds : angle 5.69317 / 3.86 ( 1234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: D 65 MET cc_start: 0.6996 (tpt) cc_final: 0.6728 (ppp) REVERT: D 75 MET cc_start: 0.8642 (mmm) cc_final: 0.8351 (mmm) REVERT: D 152 TYR cc_start: 0.7490 (p90) cc_final: 0.7268 (p90) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.0866 time to fit residues: 12.8891 Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 0.0570 chunk 80 optimal weight: 0.5980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.129088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098449 restraints weight = 16994.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101732 restraints weight = 12264.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102490 restraints weight = 7600.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102704 restraints weight = 6862.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.103232 restraints weight = 6541.808| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10247 Z= 0.138 Angle : 0.579 8.454 14104 Z= 0.313 Chirality : 0.044 0.271 1623 Planarity : 0.003 0.039 1593 Dihedral : 21.902 171.933 1944 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.76 % Allowed : 16.05 % Favored : 82.19 % 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: -1.05 (0.25), residues: 1105 helix: 0.67 (0.29), residues: 329 sheet: -1.14 (0.26), residues: 354 loop : -1.24 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 146 TYR 0.013 0.001 TYR A 211 PHE 0.008 0.001 PHE D 68 TRP 0.009 0.001 TRP D 274 HIS 0.001 0.000 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10244) covalent geometry : angle 0.57946 / 0.31 (14098) SS BOND : bond 0.00183 / 0.09 ( 3) SS BOND : angle 0.45315 / 0.30 ( 6) hydrogen bonds : bond 0.03284 / 2.15 ( 445) hydrogen bonds : angle 5.61715 / 3.80 ( 1234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: D 65 MET cc_start: 0.6986 (tpt) cc_final: 0.6723 (ppp) REVERT: D 75 MET cc_start: 0.8612 (mmm) cc_final: 0.8253 (mmm) REVERT: D 152 TYR cc_start: 0.7571 (p90) cc_final: 0.7277 (p90) outliers start: 17 outliers final: 9 residues processed: 107 average time/residue: 0.0839 time to fit residues: 13.5755 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN D 273 ASN A 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.126285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095376 restraints weight = 17058.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098666 restraints weight = 12371.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099352 restraints weight = 7615.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099546 restraints weight = 6950.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100203 restraints weight = 6631.137| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10247 Z= 0.199 Angle : 0.634 10.103 14104 Z= 0.339 Chirality : 0.046 0.284 1623 Planarity : 0.003 0.040 1593 Dihedral : 21.909 171.928 1944 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.55 % Allowed : 17.29 % Favored : 81.16 % 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: -1.12 (0.25), residues: 1105 helix: 0.61 (0.29), residues: 329 sheet: -1.29 (0.26), residues: 354 loop : -1.16 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.016 0.002 TYR B 114 PHE 0.033 0.002 PHE D 68 TRP 0.009 0.002 TRP B 28 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (10244) covalent geometry : angle 0.63425 / 0.34 (14098) SS BOND : bond 0.00150 / 0.07 ( 3) SS BOND : angle 0.61894 / 0.50 ( 6) hydrogen bonds : bond 0.03680 / 2.40 ( 445) hydrogen bonds : angle 5.73900 / 3.87 ( 1234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.376 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.0866 time to fit residues: 13.4086 Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 273 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.126366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094602 restraints weight = 16928.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097491 restraints weight = 10464.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099474 restraints weight = 7631.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100729 restraints weight = 6160.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.101678 restraints weight = 5357.076| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 10247 Z= 0.230 Angle : 0.891 59.153 14104 Z= 0.523 Chirality : 0.046 0.321 1623 Planarity : 0.004 0.047 1593 Dihedral : 21.910 171.942 1944 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.04 % Allowed : 17.60 % Favored : 81.37 % 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: -1.11 (0.25), residues: 1105 helix: 0.63 (0.29), residues: 329 sheet: -1.30 (0.26), residues: 354 loop : -1.17 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.014 0.002 TYR B 114 PHE 0.017 0.002 PHE D 68 TRP 0.009 0.002 TRP D 274 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (10244) covalent geometry : angle 0.89147 / 0.52 (14098) SS BOND : bond 0.00152 / 0.07 ( 3) SS BOND : angle 0.59917 / 0.47 ( 6) hydrogen bonds : bond 0.03682 / 2.40 ( 445) hydrogen bonds : angle 5.74023 / 3.87 ( 1234) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.391 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 95 average time/residue: 0.0891 time to fit residues: 12.7866 Evaluate side-chains 97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.126414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.094986 restraints weight = 17131.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097588 restraints weight = 13431.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098692 restraints weight = 8664.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099887 restraints weight = 7880.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100138 restraints weight = 7092.422| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 10247 Z= 0.230 Angle : 0.891 59.153 14104 Z= 0.523 Chirality : 0.046 0.321 1623 Planarity : 0.004 0.047 1593 Dihedral : 21.910 171.942 1944 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.83 % Allowed : 17.70 % Favored : 81.47 % 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: -1.11 (0.25), residues: 1105 helix: 0.63 (0.29), residues: 329 sheet: -1.30 (0.26), residues: 354 loop : -1.17 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.014 0.002 TYR B 114 PHE 0.017 0.002 PHE D 68 TRP 0.009 0.002 TRP D 274 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (10244) covalent geometry : angle 0.89147 / 0.52 (14098) SS BOND : bond 0.00152 / 0.07 ( 3) SS BOND : angle 0.59917 / 0.47 ( 6) hydrogen bonds : bond 0.03682 / 2.40 ( 445) hydrogen bonds : angle 5.74023 / 3.87 ( 1234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.90 seconds wall clock time: 28 minutes 7.61 seconds (1687.61 seconds total)