Starting phenix.real_space_refine on Wed Aug 5 13:50:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjr_39347/08_2026/8yjr_39347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjr_39347/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjr_39347/08_2026/8yjr_39347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjr_39347/08_2026/8yjr_39347.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjr_39347/08_2026/8yjr_39347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjr_39347/08_2026/8yjr_39347.cif" } 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-2.2rc3-6140/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: 2.09, per 1000 atoms: 0.21 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: 1.00 Conformation dependent library (CDL) restraints added in 311.0 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: 1.15 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: 1.67 Time building geometry restraints manager: 1.29 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: 250 5.86 - 8.79: 33 8.79 - 11.72: 8 11.72 - 14.65: 1 Bond angle restraints: 14098 Sorted by residual: angle pdb=" C3' DT E 0 " pdb=" O3' DT E 0 " pdb=" P DT E 1 " ideal model delta sigma weight residual 119.70 125.94 -6.24 1.20e+00 6.94e-01 2.70e+01 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=" C3' DA E 14 " pdb=" O3' DA E 14 " pdb=" P DA E 15 " ideal model delta sigma weight residual 119.70 125.30 -5.60 1.20e+00 6.94e-01 2.18e+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 ... (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: 3.210 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- 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= 0.353 Angle : 0.988 14.649 14104 Z= 0.625 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 0.98772 / 0.63 (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 : 0.331 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: 0.0886 time to fit residues: 18.6559 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 : 0.371 ------------------------------------------------------------------------------- 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: 4.9990 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 = 0.131386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.100939 restraints weight = 17113.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104030 restraints weight = 13131.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104396 restraints weight = 8052.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.105361 restraints weight = 7899.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105654 restraints weight = 6804.985| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10247 Z= 0.187 Angle : 0.681 7.683 14104 Z= 0.372 Chirality : 0.049 0.209 1623 Planarity : 0.005 0.051 1593 Dihedral : 21.952 169.061 1944 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.93 % Allowed : 9.73 % Favored : 89.34 % 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: -2.51 (0.22), residues: 1105 helix: -1.44 (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 0.004 0.000 ARG B 64 TYR 0.021 0.002 TYR B 133 PHE 0.023 0.002 PHE D 126 TRP 0.007 0.001 TRP C 28 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (10244) covalent geometry : angle 0.68076 / 0.37 (14098) SS BOND : bond 0.00187 / 0.09 ( 3) SS BOND : angle 1.50108 / 0.90 ( 6) hydrogen bonds : bond 0.04938 / 3.27 ( 445) hydrogen bonds : angle 7.00828 / 4.78 ( 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 : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.7831 (mmm) cc_final: 0.7627 (mmt) REVERT: D 65 MET cc_start: 0.6797 (tpt) cc_final: 0.6377 (ppp) outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.0864 time to fit residues: 14.7539 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 : 0.345 ------------------------------------------------------------------------------- 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: 0.5980 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.129463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099100 restraints weight = 17184.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.102357 restraints weight = 12373.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103183 restraints weight = 7500.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.103426 restraints weight = 6858.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103710 restraints weight = 6503.642| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10247 Z= 0.169 Angle : 0.609 7.330 14104 Z= 0.336 Chirality : 0.046 0.260 1623 Planarity : 0.004 0.049 1593 Dihedral : 21.982 171.139 1944 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.04 % Allowed : 12.73 % Favored : 86.23 % 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: -1.89 (0.23), residues: 1105 helix: -0.49 (0.27), residues: 328 sheet: -1.24 (0.27), residues: 331 loop : -1.69 (0.25), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.016 0.002 TYR A 211 PHE 0.019 0.001 PHE D 126 TRP 0.003 0.001 TRP C 28 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (10244) covalent geometry : angle 0.60918 / 0.34 (14098) SS BOND : bond 0.00241 / 0.12 ( 3) SS BOND : angle 1.07911 / 0.65 ( 6) hydrogen bonds : bond 0.04077 / 2.69 ( 445) hydrogen bonds : angle 6.41046 / 4.37 ( 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 : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 199 MET cc_start: 0.8174 (tmm) cc_final: 0.7501 (tpp) REVERT: D 37 MET cc_start: 0.7862 (mmm) cc_final: 0.7510 (mmt) REVERT: D 65 MET cc_start: 0.6873 (tpt) cc_final: 0.6571 (ppp) outliers start: 10 outliers final: 3 residues processed: 108 average time/residue: 0.0887 time to fit residues: 14.2846 Evaluate side-chains 92 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.0370 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.130315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099947 restraints weight = 17274.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101640 restraints weight = 15168.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.103328 restraints weight = 9515.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.103948 restraints weight = 7784.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104443 restraints weight = 7292.043| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10247 Z= 0.129 Angle : 0.573 6.553 14104 Z= 0.315 Chirality : 0.045 0.241 1623 Planarity : 0.004 0.045 1593 Dihedral : 21.971 171.237 1944 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.14 % Allowed : 14.39 % Favored : 84.47 % 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: -1.60 (0.24), residues: 1105 helix: -0.02 (0.28), residues: 328 sheet: -1.22 (0.27), residues: 338 loop : -1.59 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 146 TYR 0.016 0.001 TYR D 152 PHE 0.023 0.001 PHE D 68 TRP 0.005 0.001 TRP A 28 HIS 0.002 0.000 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (10244) covalent geometry : angle 0.57300 / 0.31 (14098) SS BOND : bond 0.00187 / 0.09 ( 3) SS BOND : angle 0.73545 / 0.45 ( 6) hydrogen bonds : bond 0.03556 / 2.36 ( 445) hydrogen bonds : angle 6.09930 / 4.15 ( 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 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 199 MET cc_start: 0.8140 (tmm) cc_final: 0.7842 (tmm) REVERT: D 65 MET cc_start: 0.6997 (tpt) cc_final: 0.6634 (ppp) REVERT: D 110 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7830 (mp10) outliers start: 11 outliers final: 5 residues processed: 106 average time/residue: 0.0802 time to fit residues: 12.9586 Evaluate side-chains 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASP 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: 4.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.129455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098994 restraints weight = 17134.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.102328 restraints weight = 12267.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103066 restraints weight = 7561.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103266 restraints weight = 6870.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103904 restraints weight = 6550.489| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2331 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= 0.143 Angle : 0.566 6.893 14104 Z= 0.310 Chirality : 0.045 0.243 1623 Planarity : 0.003 0.041 1593 Dihedral : 21.972 171.889 1944 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.55 % Allowed : 14.80 % Favored : 83.64 % 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: 0.27 (0.29), residues: 328 sheet: -1.22 (0.26), residues: 352 loop : -1.39 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 146 TYR 0.017 0.002 TYR B 249 PHE 0.017 0.001 PHE A 207 TRP 0.004 0.001 TRP B 28 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (10244) covalent geometry : angle 0.56566 / 0.31 (14098) SS BOND : bond 0.00414 / 0.21 ( 3) SS BOND : angle 0.51580 / 0.33 ( 6) hydrogen bonds : bond 0.03490 / 2.28 ( 445) hydrogen bonds : angle 5.88222 / 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 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 199 MET cc_start: 0.8026 (tmm) cc_final: 0.7704 (tmm) REVERT: C 199 MET cc_start: 0.8115 (tmm) cc_final: 0.7883 (tmm) REVERT: D 65 MET cc_start: 0.7010 (tpt) cc_final: 0.6678 (ppp) REVERT: D 75 MET cc_start: 0.8495 (mmm) cc_final: 0.8290 (mmm) REVERT: D 110 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7702 (mp10) outliers start: 15 outliers final: 8 residues processed: 108 average time/residue: 0.0751 time to fit residues: 11.9635 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.4554 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.130108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099684 restraints weight = 17057.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103104 restraints weight = 12202.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103803 restraints weight = 7470.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.104026 restraints weight = 6810.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.104550 restraints weight = 6463.581| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10247 Z= 0.125 Angle : 0.554 7.080 14104 Z= 0.304 Chirality : 0.044 0.243 1623 Planarity : 0.003 0.041 1593 Dihedral : 21.929 172.382 1944 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.45 % Allowed : 15.32 % Favored : 83.23 % 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: -1.23 (0.24), residues: 1105 helix: 0.46 (0.29), residues: 328 sheet: -1.18 (0.26), residues: 352 loop : -1.34 (0.27), residues: 425 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 0.024 0.001 PHE D 68 TRP 0.005 0.001 TRP C 28 HIS 0.001 0.000 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10244) covalent geometry : angle 0.55444 / 0.30 (14098) SS BOND : bond 0.00239 / 0.12 ( 3) SS BOND : angle 0.44040 / 0.28 ( 6) hydrogen bonds : bond 0.03274 / 2.15 ( 445) hydrogen bonds : angle 5.75474 / 3.91 ( 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 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.8574 (ptp) cc_final: 0.8221 (ptm) REVERT: B 199 MET cc_start: 0.7983 (tmm) cc_final: 0.7760 (tmm) REVERT: C 199 MET cc_start: 0.8096 (tmm) cc_final: 0.7803 (tmm) REVERT: D 65 MET cc_start: 0.6991 (tpt) cc_final: 0.6680 (ppp) REVERT: D 75 MET cc_start: 0.8502 (mmm) cc_final: 0.8277 (mmm) REVERT: D 110 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7776 (mp10) outliers start: 14 outliers final: 9 residues processed: 108 average time/residue: 0.0780 time to fit residues: 12.7918 Evaluate side-chains 101 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 67 MET 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 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: 0.9980 chunk 62 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN D 273 ASN A 131 GLN A 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.093630 restraints weight = 17264.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096049 restraints weight = 13809.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096924 restraints weight = 8713.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097676 restraints weight = 7827.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097839 restraints weight = 7496.578| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10247 Z= 0.260 Angle : 0.664 9.175 14104 Z= 0.353 Chirality : 0.047 0.251 1623 Planarity : 0.004 0.039 1593 Dihedral : 21.950 172.526 1944 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.86 % Allowed : 15.94 % 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: -1.28 (0.24), residues: 1105 helix: 0.42 (0.29), residues: 327 sheet: -1.32 (0.26), residues: 355 loop : -1.26 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 61 TYR 0.017 0.002 TYR A 211 PHE 0.015 0.002 PHE A 2 TRP 0.012 0.002 TRP B 28 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.26 (10244) covalent geometry : angle 0.66387 / 0.35 (14098) SS BOND : bond 0.00176 / 0.09 ( 3) SS BOND : angle 0.75153 / 0.67 ( 6) hydrogen bonds : bond 0.03950 / 2.54 ( 445) hydrogen bonds : angle 5.96944 / 4.03 ( 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 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 199 MET cc_start: 0.8290 (tmm) cc_final: 0.8072 (tmm) REVERT: D 65 MET cc_start: 0.7100 (tpt) cc_final: 0.6881 (ppp) REVERT: D 75 MET cc_start: 0.8589 (mmm) cc_final: 0.8295 (mmm) REVERT: D 110 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: D 152 TYR cc_start: 0.7794 (p90) cc_final: 0.7511 (p90) outliers start: 18 outliers final: 6 residues processed: 105 average time/residue: 0.0870 time to fit residues: 13.7979 Evaluate side-chains 92 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP 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 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: 0.5980 chunk 23 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 273 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.128154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096554 restraints weight = 16953.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.099964 restraints weight = 11998.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100528 restraints weight = 8184.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101491 restraints weight = 6832.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101610 restraints weight = 6609.150| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2859 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= 0.130 Angle : 0.585 8.521 14104 Z= 0.318 Chirality : 0.045 0.255 1623 Planarity : 0.003 0.041 1593 Dihedral : 21.856 173.034 1944 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.66 % Allowed : 16.67 % Favored : 81.68 % 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: -1.16 (0.24), residues: 1105 helix: 0.53 (0.29), residues: 330 sheet: -1.27 (0.26), residues: 352 loop : -1.18 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.019 0.001 TYR B 249 PHE 0.010 0.001 PHE A 207 TRP 0.007 0.001 TRP D 298 HIS 0.002 0.000 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (10244) covalent geometry : angle 0.58474 / 0.32 (14098) SS BOND : bond 0.00237 / 0.12 ( 3) SS BOND : angle 0.51836 / 0.32 ( 6) hydrogen bonds : bond 0.03320 / 2.18 ( 445) hydrogen bonds : angle 5.77548 / 3.91 ( 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 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 MET cc_start: 0.7088 (tpt) cc_final: 0.6805 (ppp) REVERT: D 75 MET cc_start: 0.8647 (mmm) cc_final: 0.8387 (mmm) REVERT: D 339 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7141 (mpt90) outliers start: 16 outliers final: 8 residues processed: 105 average time/residue: 0.0963 time to fit residues: 14.7764 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU 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 339 ARG 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: 2.9990 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.124905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093117 restraints weight = 17080.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096815 restraints weight = 12261.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097341 restraints weight = 8145.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.097674 restraints weight = 6761.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098111 restraints weight = 6648.434| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10247 Z= 0.226 Angle : 0.660 8.471 14104 Z= 0.348 Chirality : 0.046 0.236 1623 Planarity : 0.003 0.039 1593 Dihedral : 21.859 172.746 1944 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.35 % Allowed : 17.39 % Favored : 81.26 % 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: -1.18 (0.24), residues: 1105 helix: 0.62 (0.29), residues: 329 sheet: -1.38 (0.26), residues: 345 loop : -1.21 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.016 0.002 TYR B 249 PHE 0.032 0.002 PHE D 68 TRP 0.010 0.002 TRP B 28 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (10244) covalent geometry : angle 0.65955 / 0.35 (14098) SS BOND : bond 0.00168 / 0.08 ( 3) SS BOND : angle 0.62018 / 0.46 ( 6) hydrogen bonds : bond 0.03709 / 2.41 ( 445) hydrogen bonds : angle 5.86750 / 3.96 ( 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 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: D 339 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7327 (mpt90) outliers start: 13 outliers final: 8 residues processed: 96 average time/residue: 0.0933 time to fit residues: 13.1719 Evaluate side-chains 93 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 339 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 114 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.124982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.093219 restraints weight = 16938.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.096078 restraints weight = 10483.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.098005 restraints weight = 7631.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099335 restraints weight = 6171.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100096 restraints weight = 5335.834| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 10247 Z= 0.271 Angle : 0.911 59.199 14104 Z= 0.534 Chirality : 0.047 0.449 1623 Planarity : 0.004 0.040 1593 Dihedral : 21.861 172.775 1944 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.14 % Allowed : 18.01 % Favored : 80.85 % 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: -1.17 (0.24), residues: 1105 helix: 0.64 (0.29), residues: 329 sheet: -1.39 (0.26), residues: 345 loop : -1.19 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.016 0.002 TYR A 211 PHE 0.029 0.002 PHE D 68 TRP 0.009 0.002 TRP B 28 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.27 (10244) covalent geometry : angle 0.91068 / 0.53 (14098) SS BOND : bond 0.00164 / 0.08 ( 3) SS BOND : angle 0.60343 / 0.44 ( 6) hydrogen bonds : bond 0.03721 / 2.41 ( 445) hydrogen bonds : angle 5.87134 / 3.97 ( 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 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: D 339 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7342 (mpt90) outliers start: 11 outliers final: 8 residues processed: 93 average time/residue: 0.0958 time to fit residues: 13.1631 Evaluate side-chains 93 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 339 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 92 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.125131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093446 restraints weight = 17142.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097051 restraints weight = 12211.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.097577 restraints weight = 8218.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098153 restraints weight = 6803.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.098462 restraints weight = 6608.070| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 10247 Z= 0.271 Angle : 0.911 59.199 14104 Z= 0.534 Chirality : 0.047 0.449 1623 Planarity : 0.004 0.040 1593 Dihedral : 21.861 172.775 1944 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.93 % Allowed : 18.01 % Favored : 81.06 % 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: -1.17 (0.24), residues: 1105 helix: 0.64 (0.29), residues: 329 sheet: -1.39 (0.26), residues: 345 loop : -1.19 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.016 0.002 TYR A 211 PHE 0.029 0.002 PHE D 68 TRP 0.009 0.002 TRP B 28 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.27 (10244) covalent geometry : angle 0.91068 / 0.53 (14098) SS BOND : bond 0.00164 / 0.08 ( 3) SS BOND : angle 0.60343 / 0.44 ( 6) hydrogen bonds : bond 0.03721 / 2.41 ( 445) hydrogen bonds : angle 5.87134 / 3.97 ( 1234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.13 seconds wall clock time: 27 minutes 40.69 seconds (1660.69 seconds total)