Starting phenix.real_space_refine on Fri Sep 11 06:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vs_69850/09_2026/24vs_69850.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vs_69850/09_2026/24vs_69850.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/24vs_69850/09_2026/24vs_69850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vs_69850/09_2026/24vs_69850.map" model { file = "/net/cci-nas-00/data/ceres_data/24vs_69850/09_2026/24vs_69850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vs_69850/09_2026/24vs_69850.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= 0.008 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 5226 2.51 5 N 1276 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7866 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "C" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2006 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 4, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9PE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'YJ0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.72, per 1000 atoms: 0.22 Number of scatterers: 7866 At special positions: 0 Unit cell: (82.9521, 109.885, 118.503, 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 39 16.00 P 1 15.00 O 1324 8.00 N 1276 7.00 C 5226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 313.0 milliseconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.500A pdb=" N ARG A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 144 removed outlier: 3.940A pdb=" N THR A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.969A pdb=" N TRP A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.912A pdb=" N ALA A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 removed outlier: 4.158A pdb=" N GLN A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 244 through 257 removed outlier: 3.711A pdb=" N LEU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 283 removed outlier: 3.823A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 326 through 345 removed outlier: 3.707A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.715A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.606A pdb=" N ARG B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 removed outlier: 3.880A pdb=" N THR B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 178 removed outlier: 3.829A pdb=" N TRP B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 195 Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.609A pdb=" N ALA B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 removed outlier: 3.707A pdb=" N ILE B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 removed outlier: 3.933A pdb=" N LEU B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 283 removed outlier: 3.667A pdb=" N THR B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.541A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 345 removed outlier: 3.960A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 366 removed outlier: 3.530A pdb=" N GLY B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 removed outlier: 3.625A pdb=" N ARG C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 144 removed outlier: 4.011A pdb=" N THR C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 178 removed outlier: 3.707A pdb=" N TRP C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.564A pdb=" N ALA C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 239 removed outlier: 3.923A pdb=" N GLN C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 removed outlier: 4.035A pdb=" N LEU C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 283 removed outlier: 3.687A pdb=" N ILE C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 327 through 345 removed outlier: 4.101A pdb=" N ILE C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 333 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 366 removed outlier: 3.648A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 93 through 114 Processing helix chain 'D' and resid 117 through 145 removed outlier: 3.720A pdb=" N SER D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 183 Processing helix chain 'D' and resid 201 through 209 removed outlier: 3.877A pdb=" N LEU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.708A pdb=" N LEU D 220 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 253 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.933A pdb=" N ALA D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 326 removed outlier: 4.112A pdb=" N SER D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1163 1.31 - 1.43: 2340 1.43 - 1.56: 4509 1.56 - 1.69: 3 1.69 - 1.81: 54 Bond restraints: 8069 Sorted by residual: bond pdb=" C31 9PE C1001 " pdb=" O31 9PE C1001 " ideal model delta sigma weight residual 1.325 1.400 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C21 9PE C1001 " pdb=" O21 9PE C1001 " ideal model delta sigma weight residual 1.329 1.398 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N SER A 152 " pdb=" CA SER A 152 " ideal model delta sigma weight residual 1.459 1.418 0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" C VAL A 151 " pdb=" N SER A 152 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.27e-02 6.20e+03 5.27e+00 bond pdb=" C2 9PE C1001 " pdb=" O21 9PE C1001 " ideal model delta sigma weight residual 1.435 1.398 0.037 2.00e-02 2.50e+03 3.47e+00 ... (remaining 8064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 10703 2.55 - 5.11: 165 5.11 - 7.66: 44 7.66 - 10.21: 17 10.21 - 12.77: 2 Bond angle restraints: 10931 Sorted by residual: angle pdb=" N SER A 152 " pdb=" CA SER A 152 " pdb=" C SER A 152 " ideal model delta sigma weight residual 111.07 105.09 5.98 1.07e+00 8.73e-01 3.13e+01 angle pdb=" C LEU C 229 " pdb=" CA LEU C 229 " pdb=" CB LEU C 229 " ideal model delta sigma weight residual 117.23 110.46 6.77 1.36e+00 5.41e-01 2.48e+01 angle pdb=" CA GLU C 170 " pdb=" CB GLU C 170 " pdb=" CG GLU C 170 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CB ARG B 183 " pdb=" CG ARG B 183 " pdb=" CD ARG B 183 " ideal model delta sigma weight residual 111.30 121.06 -9.76 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CA ARG B 183 " pdb=" CB ARG B 183 " pdb=" CG ARG B 183 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 ... (remaining 10926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 4514 35.22 - 70.43: 220 70.43 - 105.65: 27 105.65 - 140.87: 31 140.87 - 176.09: 8 Dihedral angle restraints: 4800 sinusoidal: 2036 harmonic: 2764 Sorted by residual: dihedral pdb=" O30 YJ0 D 601 " pdb=" C31 YJ0 D 601 " pdb=" C32 YJ0 D 601 " pdb=" O52 YJ0 D 601 " ideal model delta sinusoidal sigma weight residual 234.92 58.83 176.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O36 YJ0 D 601 " pdb=" C31 YJ0 D 601 " pdb=" C32 YJ0 D 601 " pdb=" O52 YJ0 D 601 " ideal model delta sinusoidal sigma weight residual 124.08 -60.12 -175.80 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O51 YJ0 D 601 " pdb=" C32 YJ0 D 601 " pdb=" C33 YJ0 D 601 " pdb=" O52 YJ0 D 601 " ideal model delta sinusoidal sigma weight residual -107.97 57.02 -164.99 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.215: 1234 1.215 - 2.430: 0 2.430 - 3.646: 0 3.646 - 4.861: 0 4.861 - 6.076: 10 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C12 YJ0 D 601 " pdb=" C11 YJ0 D 601 " pdb=" C13 YJ0 D 601 " pdb=" C7 YJ0 D 601 " both_signs ideal model delta sigma weight residual False 3.10 -2.98 6.08 2.00e-01 2.50e+01 9.23e+02 chirality pdb=" C16 YJ0 D 601 " pdb=" C11 YJ0 D 601 " pdb=" C15 YJ0 D 601 " pdb=" C17 YJ0 D 601 " both_signs ideal model delta sigma weight residual False -2.82 2.75 -5.57 2.00e-01 2.50e+01 7.75e+02 chirality pdb=" C57 YJ0 D 601 " pdb=" C56 YJ0 D 601 " pdb=" C58 YJ0 D 601 " pdb=" O75 YJ0 D 601 " both_signs ideal model delta sigma weight residual False 2.67 -2.55 5.22 2.00e-01 2.50e+01 6.80e+02 ... (remaining 1241 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 D 601 " 0.094 2.00e-02 2.50e+03 7.81e-02 7.62e+01 pdb=" C18 YJ0 D 601 " -0.117 2.00e-02 2.50e+03 pdb=" C19 YJ0 D 601 " -0.044 2.00e-02 2.50e+03 pdb=" C20 YJ0 D 601 " -0.011 2.00e-02 2.50e+03 pdb=" C24 YJ0 D 601 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 121 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C TRP A 121 " 0.038 2.00e-02 2.50e+03 pdb=" O TRP A 121 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 122 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 121 " 0.011 2.00e-02 2.50e+03 1.19e-02 3.57e+00 pdb=" CG TRP A 121 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 121 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 121 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 121 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 121 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 121 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 121 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 121 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 121 " -0.000 2.00e-02 2.50e+03 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 242 2.71 - 3.26: 8136 3.26 - 3.81: 12783 3.81 - 4.35: 14709 4.35 - 4.90: 24878 Nonbonded interactions: 60748 Sorted by model distance: nonbonded pdb=" O ARG C 239 " pdb=" NH1 ARG C 239 " model vdw 2.165 3.120 nonbonded pdb=" N GLU C 260 " pdb=" OE1 GLU C 260 " model vdw 2.177 3.120 nonbonded pdb=" OG1 THR B 313 " pdb=" OH TYR C 319 " model vdw 2.208 3.040 nonbonded pdb=" NH2 ARG D 212 " pdb=" O71 YJ0 D 601 " model vdw 2.215 3.120 nonbonded pdb=" OG1 THR A 313 " pdb=" OH TYR B 319 " model vdw 2.225 3.040 ... (remaining 60743 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 110 through 366) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.440 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8069 Z= 0.210 Angle : 0.855 12.767 10931 Z= 0.409 Chirality : 0.474 6.076 1244 Planarity : 0.005 0.078 1297 Dihedral : 24.621 176.086 3030 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.96 % Favored : 92.62 % Rotamer: Outliers : 0.88 % Allowed : 28.34 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.28), residues: 948 helix: 1.49 (0.19), residues: 714 sheet: None (None), residues: 0 loop : -2.92 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 86 TYR 0.017 0.001 TYR A 125 PHE 0.018 0.001 PHE B 269 TRP 0.033 0.002 TRP A 121 HIS 0.002 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 ( 8069) covalent geometry : angle 0.85539 / 0.41 (10931) hydrogen bonds : bond 0.12531 / 7.70 ( 528) hydrogen bonds : angle 5.53786 / 4.03 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 284 LYS cc_start: 0.7858 (tptm) cc_final: 0.7534 (tppt) REVERT: C 296 MET cc_start: 0.2632 (ptp) cc_final: 0.2314 (pmm) REVERT: C 298 GLU cc_start: 0.4269 (pt0) cc_final: 0.3549 (pt0) REVERT: C 301 GLU cc_start: 0.8068 (tp30) cc_final: 0.7775 (tp30) REVERT: D 85 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6436 (tp30) REVERT: D 153 TYR cc_start: 0.6235 (p90) cc_final: 0.5835 (p90) REVERT: D 162 PHE cc_start: 0.7420 (m-80) cc_final: 0.7212 (m-80) outliers start: 7 outliers final: 4 residues processed: 149 average time/residue: 0.0977 time to fit residues: 19.1131 Evaluate side-chains 141 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 GLN C 362 GLN D 78 ASN ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.222770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.160993 restraints weight = 10558.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154952 restraints weight = 10492.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157455 restraints weight = 9378.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157434 restraints weight = 5827.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158802 restraints weight = 5339.665| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8069 Z= 0.153 Angle : 0.952 36.749 10931 Z= 0.397 Chirality : 0.086 2.182 1244 Planarity : 0.004 0.040 1297 Dihedral : 18.291 171.506 1296 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.75 % Favored : 92.93 % Rotamer: Outliers : 3.78 % Allowed : 25.06 % Favored : 71.16 % 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: 1.07 (0.28), residues: 948 helix: 1.70 (0.20), residues: 714 sheet: None (None), residues: 0 loop : -2.53 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 86 TYR 0.013 0.001 TYR D 140 PHE 0.016 0.001 PHE B 269 TRP 0.024 0.001 TRP A 327 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8069) covalent geometry : angle 0.95206 / 0.40 (10931) hydrogen bonds : bond 0.04910 / 3.24 ( 528) hydrogen bonds : angle 4.49653 / 3.28 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 MET cc_start: 0.5232 (OUTLIER) cc_final: 0.4453 (pmm) REVERT: C 327 TRP cc_start: 0.8430 (p-90) cc_final: 0.7828 (p90) REVERT: D 85 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6129 (mm-30) REVERT: D 92 PHE cc_start: 0.7965 (m-80) cc_final: 0.7759 (m-10) REVERT: D 153 TYR cc_start: 0.6072 (p90) cc_final: 0.5752 (p90) REVERT: D 162 PHE cc_start: 0.7586 (m-80) cc_final: 0.7287 (m-80) REVERT: D 167 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5840 (t80) outliers start: 30 outliers final: 13 residues processed: 164 average time/residue: 0.1019 time to fit residues: 21.6679 Evaluate side-chains 154 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 362 GLN D 78 ASN ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.219589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.157724 restraints weight = 10498.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151637 restraints weight = 9854.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152813 restraints weight = 10262.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153041 restraints weight = 6058.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154142 restraints weight = 5337.012| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8069 Z= 0.203 Angle : 0.946 34.111 10931 Z= 0.404 Chirality : 0.087 2.106 1244 Planarity : 0.004 0.048 1297 Dihedral : 17.642 172.506 1289 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.96 % Favored : 92.83 % Rotamer: Outliers : 4.03 % Allowed : 25.69 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.28), residues: 948 helix: 1.52 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.82 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 117 TYR 0.025 0.001 TYR A 125 PHE 0.015 0.002 PHE A 277 TRP 0.029 0.001 TRP A 327 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 8069) covalent geometry : angle 0.94577 / 0.40 (10931) hydrogen bonds : bond 0.05089 / 3.39 ( 528) hydrogen bonds : angle 4.48886 / 3.28 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4577 (pmm) REVERT: B 174 ARG cc_start: 0.7417 (ptm-80) cc_final: 0.6552 (ptt180) REVERT: D 153 TYR cc_start: 0.6519 (p90) cc_final: 0.6257 (p90) REVERT: D 162 PHE cc_start: 0.7798 (m-80) cc_final: 0.7396 (m-80) REVERT: D 167 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6171 (t80) outliers start: 32 outliers final: 20 residues processed: 167 average time/residue: 0.0927 time to fit residues: 20.5686 Evaluate side-chains 166 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 34 optimal weight: 7.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS C 362 GLN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.221841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159931 restraints weight = 10743.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.155461 restraints weight = 10236.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157363 restraints weight = 9570.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157285 restraints weight = 5849.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.158611 restraints weight = 5286.799| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8069 Z= 0.145 Angle : 0.917 34.160 10931 Z= 0.385 Chirality : 0.085 2.079 1244 Planarity : 0.004 0.046 1297 Dihedral : 17.342 171.328 1289 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.43 % Favored : 93.35 % Rotamer: Outliers : 4.16 % Allowed : 25.69 % Favored : 70.15 % 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: 1.02 (0.28), residues: 948 helix: 1.69 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -2.83 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 236 TYR 0.010 0.001 TYR C 280 PHE 0.013 0.001 PHE B 269 TRP 0.030 0.001 TRP A 327 HIS 0.001 0.000 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8069) covalent geometry : angle 0.91670 / 0.38 (10931) hydrogen bonds : bond 0.04618 / 3.05 ( 528) hydrogen bonds : angle 4.37187 / 3.18 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.6772 (m-80) cc_final: 0.6489 (m-80) REVERT: A 259 LYS cc_start: 0.8029 (mptt) cc_final: 0.7678 (tptm) REVERT: A 296 MET cc_start: 0.5182 (OUTLIER) cc_final: 0.4498 (pmm) REVERT: C 270 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8389 (mt) REVERT: D 162 PHE cc_start: 0.7741 (m-80) cc_final: 0.7477 (m-80) REVERT: D 167 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6066 (t80) outliers start: 33 outliers final: 19 residues processed: 165 average time/residue: 0.0927 time to fit residues: 20.2833 Evaluate side-chains 164 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 78 ASN ** D 320 GLN ** 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 = 0.4472 r_free = 0.4472 target = 0.216917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139668 restraints weight = 10554.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135079 restraints weight = 7315.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137029 restraints weight = 6972.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138156 restraints weight = 5536.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137917 restraints weight = 5190.086| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.006 0.054 8069 Z= 0.257 Angle : 0.986 34.446 10931 Z= 0.427 Chirality : 0.086 2.045 1244 Planarity : 0.004 0.054 1297 Dihedral : 17.280 170.995 1289 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.17 % Favored : 92.62 % Rotamer: Outliers : 4.91 % Allowed : 25.82 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.28), residues: 948 helix: 1.44 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -2.95 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 239 TYR 0.017 0.002 TYR A 125 PHE 0.019 0.002 PHE C 277 TRP 0.032 0.002 TRP A 327 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.26 ( 8069) covalent geometry : angle 0.98626 / 0.43 (10931) hydrogen bonds : bond 0.05525 / 3.70 ( 528) hydrogen bonds : angle 4.57374 / 3.31 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.172 Fit side-chains REVERT: A 148 TYR cc_start: 0.6845 (m-80) cc_final: 0.6338 (m-80) REVERT: A 192 LYS cc_start: 0.5895 (ttpp) cc_final: 0.5467 (ttpp) REVERT: A 259 LYS cc_start: 0.8144 (mptt) cc_final: 0.7599 (tptm) REVERT: A 296 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.4566 (pmm) REVERT: B 174 ARG cc_start: 0.7627 (ptm-80) cc_final: 0.6757 (ptt180) REVERT: B 236 ARG cc_start: 0.7435 (ptt90) cc_final: 0.7221 (ptt90) REVERT: B 239 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7475 (tmt-80) REVERT: C 270 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8478 (mt) REVERT: D 85 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: D 167 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6554 (t80) REVERT: D 322 GLN cc_start: 0.7818 (pp30) cc_final: 0.7608 (pp30) outliers start: 39 outliers final: 27 residues processed: 165 average time/residue: 0.0937 time to fit residues: 20.4566 Evaluate side-chains 168 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS D 78 ASN ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.225262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.166759 restraints weight = 10817.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.159728 restraints weight = 11283.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.162170 restraints weight = 10175.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.162021 restraints weight = 6080.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.163355 restraints weight = 5488.710| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8069 Z= 0.140 Angle : 0.921 33.857 10931 Z= 0.387 Chirality : 0.084 2.044 1244 Planarity : 0.004 0.048 1297 Dihedral : 17.077 172.028 1289 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.65 % Favored : 93.14 % Rotamer: Outliers : 4.03 % Allowed : 27.33 % Favored : 68.64 % 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: 0.92 (0.28), residues: 948 helix: 1.60 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -3.07 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 239 TYR 0.011 0.001 TYR A 280 PHE 0.021 0.001 PHE B 269 TRP 0.034 0.001 TRP A 327 HIS 0.002 0.000 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 8069) covalent geometry : angle 0.92061 / 0.39 (10931) hydrogen bonds : bond 0.04569 / 3.01 ( 528) hydrogen bonds : angle 4.41938 / 3.20 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.312 Fit side-chains REVERT: A 148 TYR cc_start: 0.6762 (m-80) cc_final: 0.6491 (m-80) REVERT: A 192 LYS cc_start: 0.5765 (ttpp) cc_final: 0.5198 (ttpp) REVERT: A 259 LYS cc_start: 0.8058 (mptt) cc_final: 0.7696 (tptm) REVERT: A 296 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4356 (pmm) REVERT: D 85 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6585 (mm-30) REVERT: D 162 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: D 167 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6045 (t80) REVERT: D 209 ARG cc_start: 0.6170 (tmm-80) cc_final: 0.5364 (tmm-80) REVERT: D 322 GLN cc_start: 0.7727 (pp30) cc_final: 0.7456 (pp30) outliers start: 32 outliers final: 21 residues processed: 165 average time/residue: 0.1054 time to fit residues: 22.8121 Evaluate side-chains 164 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 78 ASN D 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.222293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.162871 restraints weight = 10904.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156975 restraints weight = 11842.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158552 restraints weight = 10856.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158169 restraints weight = 6320.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160610 restraints weight = 5576.081| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8069 Z= 0.213 Angle : 0.958 34.127 10931 Z= 0.410 Chirality : 0.085 2.026 1244 Planarity : 0.004 0.048 1297 Dihedral : 17.106 172.249 1289 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.65 % Favored : 93.04 % Rotamer: Outliers : 5.29 % Allowed : 26.20 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.28), residues: 948 helix: 1.50 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -2.89 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 239 TYR 0.009 0.001 TYR D 73 PHE 0.018 0.002 PHE B 269 TRP 0.033 0.002 TRP A 327 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 8069) covalent geometry : angle 0.95766 / 0.41 (10931) hydrogen bonds : bond 0.05110 / 3.41 ( 528) hydrogen bonds : angle 4.49410 / 3.25 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.4974 (mt) REVERT: A 148 TYR cc_start: 0.6755 (m-80) cc_final: 0.6454 (m-80) REVERT: A 192 LYS cc_start: 0.5759 (ttpp) cc_final: 0.5185 (ttpp) REVERT: A 200 MET cc_start: 0.8303 (tpt) cc_final: 0.8034 (tpp) REVERT: A 240 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6835 (tpt) REVERT: A 259 LYS cc_start: 0.8146 (mptt) cc_final: 0.7718 (tptm) REVERT: A 296 MET cc_start: 0.5044 (OUTLIER) cc_final: 0.4461 (pmm) REVERT: B 174 ARG cc_start: 0.7232 (ptm-80) cc_final: 0.6518 (ptt180) REVERT: B 239 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7436 (tmt-80) REVERT: C 126 HIS cc_start: 0.3654 (t-170) cc_final: 0.3020 (m170) REVERT: D 85 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: D 162 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: D 167 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6060 (t80) REVERT: D 209 ARG cc_start: 0.6182 (tmm-80) cc_final: 0.5402 (tmm-80) REVERT: D 322 GLN cc_start: 0.7885 (pp30) cc_final: 0.7641 (pp30) outliers start: 42 outliers final: 26 residues processed: 169 average time/residue: 0.1037 time to fit residues: 22.9433 Evaluate side-chains 172 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 20 optimal weight: 0.1980 chunk 79 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.226155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.167426 restraints weight = 10951.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161965 restraints weight = 10906.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163814 restraints weight = 9580.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164945 restraints weight = 5929.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.165722 restraints weight = 5294.502| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8069 Z= 0.138 Angle : 0.930 33.663 10931 Z= 0.393 Chirality : 0.084 2.028 1244 Planarity : 0.004 0.043 1297 Dihedral : 17.068 173.262 1289 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.54 % Favored : 93.14 % Rotamer: Outliers : 4.03 % Allowed : 27.46 % Favored : 68.51 % 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: 1.01 (0.29), residues: 948 helix: 1.61 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -2.95 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 236 TYR 0.008 0.001 TYR C 280 PHE 0.019 0.001 PHE B 269 TRP 0.035 0.001 TRP A 327 HIS 0.001 0.000 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 8069) covalent geometry : angle 0.92996 / 0.39 (10931) hydrogen bonds : bond 0.04425 / 2.92 ( 528) hydrogen bonds : angle 4.36407 / 3.16 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 148 TYR cc_start: 0.6740 (m-80) cc_final: 0.6468 (m-80) REVERT: A 192 LYS cc_start: 0.5754 (ttpp) cc_final: 0.5131 (ttpp) REVERT: A 240 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6865 (tpt) REVERT: A 259 LYS cc_start: 0.8062 (mptt) cc_final: 0.7681 (tptm) REVERT: A 296 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.4335 (pmm) REVERT: C 126 HIS cc_start: 0.3618 (t-170) cc_final: 0.3020 (m170) REVERT: D 85 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6728 (mm-30) REVERT: D 162 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: D 167 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.5919 (t80) REVERT: D 209 ARG cc_start: 0.6090 (tmm-80) cc_final: 0.5316 (tmm-80) REVERT: D 322 GLN cc_start: 0.7818 (pp30) cc_final: 0.7562 (pp30) outliers start: 32 outliers final: 23 residues processed: 167 average time/residue: 0.0937 time to fit residues: 20.6835 Evaluate side-chains 166 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.226135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.166565 restraints weight = 10912.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161850 restraints weight = 10795.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164045 restraints weight = 9587.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.164153 restraints weight = 5952.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165268 restraints weight = 5516.420| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8069 Z= 0.147 Angle : 0.946 33.582 10931 Z= 0.402 Chirality : 0.084 2.019 1244 Planarity : 0.004 0.041 1297 Dihedral : 17.063 173.464 1289 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.54 % Favored : 93.14 % Rotamer: Outliers : 3.78 % Allowed : 27.58 % Favored : 68.64 % 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: 1.10 (0.29), residues: 948 helix: 1.65 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -2.75 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 239 TYR 0.013 0.001 TYR D 73 PHE 0.018 0.001 PHE B 269 TRP 0.042 0.001 TRP A 327 HIS 0.002 0.000 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 8069) covalent geometry : angle 0.94641 / 0.40 (10931) hydrogen bonds : bond 0.04516 / 2.99 ( 528) hydrogen bonds : angle 4.35090 / 3.15 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 148 TYR cc_start: 0.6725 (m-80) cc_final: 0.6451 (m-80) REVERT: A 192 LYS cc_start: 0.5652 (ttpp) cc_final: 0.4977 (ttpp) REVERT: A 240 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6877 (tpt) REVERT: A 259 LYS cc_start: 0.8053 (mptt) cc_final: 0.7673 (tptm) REVERT: A 296 MET cc_start: 0.5001 (OUTLIER) cc_final: 0.4341 (pmm) REVERT: A 360 GLN cc_start: 0.8761 (tt0) cc_final: 0.8522 (tt0) REVERT: B 232 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7529 (mt) REVERT: B 239 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7413 (tmt-80) REVERT: C 126 HIS cc_start: 0.3613 (t-170) cc_final: 0.2977 (m170) REVERT: C 240 MET cc_start: 0.5234 (mmm) cc_final: 0.4895 (mmt) REVERT: D 85 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: D 162 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: D 167 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5938 (t80) REVERT: D 209 ARG cc_start: 0.6097 (tmm-80) cc_final: 0.5349 (tmm-80) REVERT: D 210 MET cc_start: 0.7616 (tpt) cc_final: 0.7387 (tpp) REVERT: D 322 GLN cc_start: 0.7739 (pp30) cc_final: 0.7495 (pp30) outliers start: 30 outliers final: 22 residues processed: 162 average time/residue: 0.0998 time to fit residues: 21.2244 Evaluate side-chains 169 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.0060 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.226547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.166617 restraints weight = 10522.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163386 restraints weight = 9420.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165113 restraints weight = 8860.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165377 restraints weight = 5448.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.166264 restraints weight = 5033.084| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8069 Z= 0.137 Angle : 0.942 33.439 10931 Z= 0.399 Chirality : 0.084 2.008 1244 Planarity : 0.004 0.044 1297 Dihedral : 16.948 174.026 1289 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.43 % Favored : 93.25 % Rotamer: Outliers : 3.40 % Allowed : 27.58 % Favored : 69.02 % 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: 1.15 (0.29), residues: 948 helix: 1.73 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -2.75 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 239 TYR 0.010 0.001 TYR D 73 PHE 0.018 0.001 PHE B 269 TRP 0.025 0.001 TRP A 327 HIS 0.001 0.000 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 8069) covalent geometry : angle 0.94244 / 0.40 (10931) hydrogen bonds : bond 0.04324 / 2.86 ( 528) hydrogen bonds : angle 4.28721 / 3.10 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.5778 (m-80) cc_final: 0.5383 (m-80) REVERT: A 192 LYS cc_start: 0.5575 (ttpp) cc_final: 0.4855 (ttpp) REVERT: A 240 MET cc_start: 0.7663 (tpt) cc_final: 0.6883 (tpt) REVERT: A 259 LYS cc_start: 0.7954 (mptt) cc_final: 0.7579 (tptm) REVERT: A 296 MET cc_start: 0.5003 (OUTLIER) cc_final: 0.4311 (pmm) REVERT: B 232 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7527 (mt) REVERT: B 239 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7333 (tmt-80) REVERT: C 126 HIS cc_start: 0.3582 (t-170) cc_final: 0.2974 (m170) REVERT: C 296 MET cc_start: 0.2617 (ptp) cc_final: 0.2223 (pmm) REVERT: D 162 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: D 167 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.5749 (t80) REVERT: D 209 ARG cc_start: 0.6058 (tmm-80) cc_final: 0.5340 (tmm-80) REVERT: D 322 GLN cc_start: 0.7701 (pp30) cc_final: 0.7469 (pp30) outliers start: 27 outliers final: 21 residues processed: 159 average time/residue: 0.0987 time to fit residues: 20.7035 Evaluate side-chains 164 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 0.0170 chunk 67 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.225745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165658 restraints weight = 10898.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161555 restraints weight = 10551.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163365 restraints weight = 9532.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.164156 restraints weight = 6034.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168431 restraints weight = 5296.641| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8069 Z= 0.161 Angle : 0.957 33.504 10931 Z= 0.409 Chirality : 0.084 2.002 1244 Planarity : 0.004 0.042 1297 Dihedral : 16.970 174.219 1289 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.54 % Favored : 93.14 % Rotamer: Outliers : 3.65 % Allowed : 27.58 % Favored : 68.77 % 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: 1.09 (0.28), residues: 948 helix: 1.70 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -2.78 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 236 TYR 0.008 0.001 TYR D 73 PHE 0.017 0.001 PHE B 269 TRP 0.032 0.001 TRP A 327 HIS 0.001 0.000 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 8069) covalent geometry : angle 0.95682 / 0.41 (10931) hydrogen bonds : bond 0.04534 / 3.01 ( 528) hydrogen bonds : angle 4.30409 / 3.11 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1370.20 seconds wall clock time: 24 minutes 22.41 seconds (1462.41 seconds total)