Starting phenix.real_space_refine on Tue Feb 3 18:19:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e07_47351/02_2026/9e07_47351.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e07_47351/02_2026/9e07_47351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e07_47351/02_2026/9e07_47351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e07_47351/02_2026/9e07_47351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e07_47351/02_2026/9e07_47351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e07_47351/02_2026/9e07_47351.map" } resolution = 3.4 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 4119 2.51 5 N 888 2.21 5 O 948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5976 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1868 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 1 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1868 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 1 Chain: "E" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1868 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 1.49, per 1000 atoms: 0.25 Number of scatterers: 5976 At special positions: 0 Unit cell: (101.504, 94.016, 80.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 948 8.00 N 888 7.00 C 4119 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: 0.49 Conformation dependent library (CDL) restraints added in 323.3 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 1 sheets defined 86.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.673A pdb=" N ILE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 9 through 33 Processing helix chain 'A' and resid 33 through 60 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 165 through 183 Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.645A pdb=" N ILE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 228 removed outlier: 4.403A pdb=" N LEU A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.647A pdb=" N PHE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 removed outlier: 3.904A pdb=" N GLY A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.760A pdb=" N TYR A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.711A pdb=" N LEU A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 307 removed outlier: 3.587A pdb=" N VAL A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 333 Proline residue: A 321 - end of helix Processing helix chain 'C' and resid 6 through 8 No H-bonds generated for 'chain 'C' and resid 6 through 8' Processing helix chain 'C' and resid 9 through 33 Processing helix chain 'C' and resid 33 through 60 Proline residue: C 44 - end of helix Processing helix chain 'C' and resid 165 through 183 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.663A pdb=" N ILE C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 228 removed outlier: 4.224A pdb=" N LEU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.634A pdb=" N PHE C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 269 removed outlier: 3.762A pdb=" N GLY C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.759A pdb=" N TYR C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.693A pdb=" N LEU C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 307 removed outlier: 3.830A pdb=" N ALA C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 298 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 333 Proline residue: C 321 - end of helix Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 9 through 33 Processing helix chain 'E' and resid 33 through 60 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 165 through 183 Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.583A pdb=" N TRP E 189 " --> pdb=" O PRO E 185 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 3.984A pdb=" N LEU E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Proline residue: E 209 - end of helix removed outlier: 3.513A pdb=" N ILE E 220 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 241 removed outlier: 3.652A pdb=" N PHE E 232 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 282 removed outlier: 4.262A pdb=" N GLY E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) Proline residue: E 272 - end of helix removed outlier: 3.674A pdb=" N ALA E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR E 276 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 280 " --> pdb=" O TYR E 276 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 removed outlier: 3.575A pdb=" N LEU E 289 " --> pdb=" O THR E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 308 removed outlier: 3.635A pdb=" N VAL E 298 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 299 " --> pdb=" O TYR E 295 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU E 302 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 333 Proline residue: E 321 - end of helix removed outlier: 3.678A pdb=" N LEU E 331 " --> pdb=" O GLY E 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'D' and resid 8 through 19 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 3.968A pdb=" N MET A 158 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 249 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR A 246 " --> pdb=" O THR E 161 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET E 158 " --> pdb=" O PRO E 247 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 249 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET C 158 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 249 " --> pdb=" O MET C 158 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1326 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: 0.92 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1698 1.34 - 1.46: 1494 1.46 - 1.58: 2907 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 6141 Sorted by residual: bond pdb=" CB TYR A 276 " pdb=" CG TYR A 276 " ideal model delta sigma weight residual 1.512 1.529 -0.017 2.20e-02 2.07e+03 6.14e-01 bond pdb=" CB PRO A 44 " pdb=" CG PRO A 44 " ideal model delta sigma weight residual 1.492 1.459 0.033 5.00e-02 4.00e+02 4.29e-01 bond pdb=" C THR A 230 " pdb=" N PRO A 231 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.07e-01 bond pdb=" C LYS C 6 " pdb=" N PRO C 7 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.59e-01 bond pdb=" CG PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.56e-01 ... (remaining 6136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 8221 1.60 - 3.21: 105 3.21 - 4.81: 9 4.81 - 6.42: 25 6.42 - 8.02: 1 Bond angle restraints: 8361 Sorted by residual: angle pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " pdb=" CG LEU A 283 " ideal model delta sigma weight residual 116.30 124.32 -8.02 3.50e+00 8.16e-02 5.25e+00 angle pdb=" CA TYR A 276 " pdb=" CB TYR A 276 " pdb=" CG TYR A 276 " ideal model delta sigma weight residual 113.90 117.98 -4.08 1.80e+00 3.09e-01 5.14e+00 angle pdb=" CA LEU A 219 " pdb=" CB LEU A 219 " pdb=" CG LEU A 219 " ideal model delta sigma weight residual 116.30 122.70 -6.40 3.50e+00 8.16e-02 3.34e+00 angle pdb=" CA LEU E 283 " pdb=" CB LEU E 283 " pdb=" CG LEU E 283 " ideal model delta sigma weight residual 116.30 122.64 -6.34 3.50e+00 8.16e-02 3.28e+00 angle pdb=" CB MET A 217 " pdb=" CG MET A 217 " pdb=" SD MET A 217 " ideal model delta sigma weight residual 112.70 117.87 -5.17 3.00e+00 1.11e-01 2.96e+00 ... (remaining 8356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 2997 16.51 - 33.02: 352 33.02 - 49.53: 110 49.53 - 66.04: 27 66.04 - 82.55: 3 Dihedral angle restraints: 3489 sinusoidal: 1323 harmonic: 2166 Sorted by residual: dihedral pdb=" CA PRO C 272 " pdb=" C PRO C 272 " pdb=" N VAL C 273 " pdb=" CA VAL C 273 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO A 272 " pdb=" C PRO A 272 " pdb=" N VAL A 273 " pdb=" CA VAL A 273 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" N LEU C 302 " pdb=" CA LEU C 302 " pdb=" CB LEU C 302 " pdb=" CG LEU C 302 " ideal model delta sinusoidal sigma weight residual -180.00 -120.30 -59.70 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 731 0.037 - 0.075: 214 0.075 - 0.112: 61 0.112 - 0.150: 7 0.150 - 0.187: 1 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CB THR C 259 " pdb=" CA THR C 259 " pdb=" OG1 THR C 259 " pdb=" CG2 THR C 259 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CB THR A 314 " pdb=" CA THR A 314 " pdb=" OG1 THR A 314 " pdb=" CG2 THR A 314 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CB ILE A 18 " pdb=" CA ILE A 18 " pdb=" CG1 ILE A 18 " pdb=" CG2 ILE A 18 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1011 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 308 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO A 309 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 273 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C VAL A 273 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL A 273 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 274 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 273 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C VAL C 273 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL C 273 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL C 274 " -0.007 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 740 2.75 - 3.28: 5989 3.28 - 3.82: 10083 3.82 - 4.36: 10705 4.36 - 4.90: 18864 Nonbonded interactions: 46381 Sorted by model distance: nonbonded pdb=" O ALA C 304 " pdb=" OG1 THR C 308 " model vdw 2.208 3.040 nonbonded pdb=" O VAL C 333 " pdb=" ND1 HIS C 334 " model vdw 2.234 3.120 nonbonded pdb=" O ASP E 311 " pdb=" OG1 THR E 314 " model vdw 2.247 3.040 nonbonded pdb=" O VAL A 333 " pdb=" ND1 HIS A 334 " model vdw 2.249 3.120 nonbonded pdb=" O VAL E 333 " pdb=" ND1 HIS E 334 " model vdw 2.304 3.120 ... (remaining 46376 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.003 0.033 6141 Z= 0.118 Angle : 0.520 8.023 8361 Z= 0.254 Chirality : 0.039 0.187 1014 Planarity : 0.004 0.036 990 Dihedral : 16.199 82.550 2097 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 6.45 % Allowed : 25.16 % Favored : 68.40 % 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 (0.33), residues: 738 helix: 1.51 (0.23), residues: 579 sheet: None (None), residues: 0 loop : -2.36 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 15 TYR 0.009 0.001 TYR A 226 PHE 0.018 0.001 PHE A 27 TRP 0.010 0.001 TRP A 189 HIS 0.003 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6141) covalent geometry : angle 0.52017 ( 8361) hydrogen bonds : bond 0.17524 ( 444) hydrogen bonds : angle 6.14788 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.217 Fit side-chains REVERT: A 54 LYS cc_start: 0.8277 (mmtp) cc_final: 0.7794 (mmtp) REVERT: A 203 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: A 212 VAL cc_start: 0.8507 (t) cc_final: 0.8287 (p) REVERT: A 334 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7576 (m-70) REVERT: C 54 LYS cc_start: 0.8331 (mmtp) cc_final: 0.7872 (mmtp) REVERT: C 191 LEU cc_start: 0.8565 (tp) cc_final: 0.8318 (tt) REVERT: C 208 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7864 (mm) REVERT: C 212 VAL cc_start: 0.8413 (t) cc_final: 0.8183 (p) REVERT: C 271 LEU cc_start: 0.8095 (mt) cc_final: 0.7738 (mm) REVERT: C 298 VAL cc_start: 0.8083 (m) cc_final: 0.7742 (p) REVERT: C 299 ILE cc_start: 0.8159 (pt) cc_final: 0.7951 (mp) REVERT: C 307 LEU cc_start: 0.8010 (mt) cc_final: 0.7759 (mt) REVERT: E 5 MET cc_start: 0.7282 (mpp) cc_final: 0.7043 (mmm) REVERT: E 23 VAL cc_start: 0.8384 (t) cc_final: 0.8178 (m) REVERT: E 267 ILE cc_start: 0.8215 (mt) cc_final: 0.7952 (mm) REVERT: E 318 MET cc_start: 0.8143 (tpp) cc_final: 0.7611 (tpp) REVERT: E 326 TYR cc_start: 0.8474 (t80) cc_final: 0.8258 (t80) REVERT: E 329 SER cc_start: 0.9029 (t) cc_final: 0.8815 (m) REVERT: E 331 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7930 (mm) REVERT: E 334 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.6149 (m90) outliers start: 41 outliers final: 34 residues processed: 217 average time/residue: 0.0443 time to fit residues: 14.7001 Evaluate side-chains 230 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain D residue 19 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.0030 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.0370 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103430 restraints weight = 9835.256| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.16 r_work: 0.3152 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6141 Z= 0.115 Angle : 0.526 6.987 8361 Z= 0.262 Chirality : 0.039 0.136 1014 Planarity : 0.004 0.033 990 Dihedral : 9.331 59.511 858 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 7.86 % Allowed : 22.33 % Favored : 69.81 % 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: 1.70 (0.33), residues: 738 helix: 1.94 (0.22), residues: 603 sheet: None (None), residues: 0 loop : -2.80 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.007 0.001 TYR A 226 PHE 0.014 0.001 PHE C 27 TRP 0.017 0.001 TRP E 189 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6141) covalent geometry : angle 0.52600 ( 8361) hydrogen bonds : bond 0.03558 ( 444) hydrogen bonds : angle 4.05702 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.214 Fit side-chains REVERT: F 7 TRP cc_start: 0.6870 (OUTLIER) cc_final: 0.6666 (t60) REVERT: A 54 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7826 (mmtp) REVERT: A 203 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6262 (pm20) REVERT: A 208 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 212 VAL cc_start: 0.8472 (t) cc_final: 0.8241 (p) REVERT: A 267 ILE cc_start: 0.8277 (mt) cc_final: 0.8059 (mm) REVERT: A 302 LEU cc_start: 0.8433 (tp) cc_final: 0.8047 (tt) REVERT: C 54 LYS cc_start: 0.8337 (mmtp) cc_final: 0.7906 (mmtp) REVERT: C 191 LEU cc_start: 0.8562 (tp) cc_final: 0.8313 (tt) REVERT: C 212 VAL cc_start: 0.8440 (t) cc_final: 0.8212 (p) REVERT: C 271 LEU cc_start: 0.8083 (mt) cc_final: 0.7728 (mm) REVERT: C 298 VAL cc_start: 0.8306 (m) cc_final: 0.8002 (p) REVERT: E 5 MET cc_start: 0.7176 (mpp) cc_final: 0.6942 (mmm) REVERT: E 203 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.6047 (pm20) REVERT: E 206 MET cc_start: 0.7958 (mtm) cc_final: 0.7551 (mtm) REVERT: E 208 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8176 (mm) REVERT: E 220 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8152 (tt) REVERT: E 300 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8403 (tt) REVERT: E 318 MET cc_start: 0.8058 (tpp) cc_final: 0.7607 (tpp) REVERT: E 329 SER cc_start: 0.8781 (t) cc_final: 0.8427 (m) outliers start: 50 outliers final: 29 residues processed: 227 average time/residue: 0.0462 time to fit residues: 15.8728 Evaluate side-chains 231 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 TRP Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101540 restraints weight = 9735.543| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.15 r_work: 0.3124 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6141 Z= 0.152 Angle : 0.524 6.763 8361 Z= 0.267 Chirality : 0.040 0.132 1014 Planarity : 0.004 0.037 990 Dihedral : 7.499 56.649 814 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 8.33 % Allowed : 25.00 % Favored : 66.67 % 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: 1.83 (0.33), residues: 738 helix: 1.98 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.60 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.008 0.001 TYR A 226 PHE 0.022 0.001 PHE A 27 TRP 0.012 0.001 TRP E 189 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6141) covalent geometry : angle 0.52440 ( 8361) hydrogen bonds : bond 0.03818 ( 444) hydrogen bonds : angle 3.89015 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.263 Fit side-chains REVERT: A 54 LYS cc_start: 0.8407 (mmtp) cc_final: 0.7930 (mmtp) REVERT: A 203 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6406 (pm20) REVERT: A 208 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 212 VAL cc_start: 0.8565 (t) cc_final: 0.8324 (p) REVERT: A 267 ILE cc_start: 0.8411 (mt) cc_final: 0.8200 (mm) REVERT: A 298 VAL cc_start: 0.8543 (t) cc_final: 0.8294 (p) REVERT: A 302 LEU cc_start: 0.8524 (tp) cc_final: 0.8156 (tt) REVERT: A 334 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7295 (m-70) REVERT: C 54 LYS cc_start: 0.8443 (mmtp) cc_final: 0.7969 (mmtp) REVERT: C 191 LEU cc_start: 0.8663 (tp) cc_final: 0.8438 (tt) REVERT: C 271 LEU cc_start: 0.8192 (mt) cc_final: 0.7740 (mm) REVERT: C 298 VAL cc_start: 0.8368 (m) cc_final: 0.8086 (p) REVERT: E 5 MET cc_start: 0.7243 (mpp) cc_final: 0.7005 (mmm) REVERT: E 203 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6080 (pm20) REVERT: E 206 MET cc_start: 0.8158 (mtm) cc_final: 0.7676 (mtm) REVERT: E 318 MET cc_start: 0.8274 (tpp) cc_final: 0.7912 (tpp) REVERT: E 322 LEU cc_start: 0.8616 (mt) cc_final: 0.8331 (mp) REVERT: E 329 SER cc_start: 0.8800 (t) cc_final: 0.8462 (m) outliers start: 53 outliers final: 33 residues processed: 226 average time/residue: 0.0446 time to fit residues: 15.3542 Evaluate side-chains 231 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 60 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103029 restraints weight = 9853.877| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.18 r_work: 0.3121 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6141 Z= 0.143 Angle : 0.522 6.873 8361 Z= 0.264 Chirality : 0.040 0.135 1014 Planarity : 0.004 0.039 990 Dihedral : 7.382 54.974 814 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 8.81 % Allowed : 25.00 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.33), residues: 738 helix: 1.99 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -2.75 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.006 0.001 TYR A 226 PHE 0.018 0.001 PHE E 27 TRP 0.014 0.001 TRP E 189 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6141) covalent geometry : angle 0.52173 ( 8361) hydrogen bonds : bond 0.03561 ( 444) hydrogen bonds : angle 3.82697 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.242 Fit side-chains REVERT: A 54 LYS cc_start: 0.8332 (mmtp) cc_final: 0.7855 (mmtp) REVERT: A 208 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8122 (mm) REVERT: A 212 VAL cc_start: 0.8502 (t) cc_final: 0.8281 (p) REVERT: A 298 VAL cc_start: 0.8499 (t) cc_final: 0.8259 (p) REVERT: A 302 LEU cc_start: 0.8427 (tp) cc_final: 0.8046 (tt) REVERT: A 334 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7160 (m-70) REVERT: C 54 LYS cc_start: 0.8368 (mmtp) cc_final: 0.7902 (mmtp) REVERT: C 191 LEU cc_start: 0.8608 (tp) cc_final: 0.8370 (tt) REVERT: C 271 LEU cc_start: 0.8151 (mt) cc_final: 0.7765 (mm) REVERT: C 298 VAL cc_start: 0.8345 (m) cc_final: 0.8057 (p) REVERT: E 5 MET cc_start: 0.7229 (mpp) cc_final: 0.6991 (mmm) REVERT: E 172 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8132 (mp) REVERT: E 203 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5780 (pm20) REVERT: E 206 MET cc_start: 0.7940 (mtm) cc_final: 0.7433 (mtm) REVERT: E 318 MET cc_start: 0.8028 (tpp) cc_final: 0.7645 (tpp) REVERT: E 332 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8255 (mt) outliers start: 56 outliers final: 36 residues processed: 222 average time/residue: 0.0463 time to fit residues: 15.5415 Evaluate side-chains 234 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102537 restraints weight = 10013.118| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.16 r_work: 0.3132 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6141 Z= 0.124 Angle : 0.514 6.540 8361 Z= 0.258 Chirality : 0.039 0.141 1014 Planarity : 0.004 0.040 990 Dihedral : 7.147 53.560 811 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 9.43 % Allowed : 24.21 % Favored : 66.35 % 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: 1.96 (0.33), residues: 738 helix: 2.10 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -2.82 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.006 0.001 TYR A 226 PHE 0.017 0.001 PHE E 27 TRP 0.012 0.001 TRP A 189 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6141) covalent geometry : angle 0.51391 ( 8361) hydrogen bonds : bond 0.03330 ( 444) hydrogen bonds : angle 3.74751 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 0.222 Fit side-chains REVERT: F 7 TRP cc_start: 0.6999 (OUTLIER) cc_final: 0.6798 (t60) REVERT: A 54 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7827 (mmtp) REVERT: A 184 MET cc_start: 0.8161 (mmm) cc_final: 0.7784 (tpp) REVERT: A 203 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6201 (pm20) REVERT: A 208 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 212 VAL cc_start: 0.8498 (t) cc_final: 0.8267 (p) REVERT: A 267 ILE cc_start: 0.8348 (mt) cc_final: 0.8137 (mm) REVERT: A 298 VAL cc_start: 0.8488 (t) cc_final: 0.8257 (p) REVERT: A 334 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.6965 (m-70) REVERT: C 54 LYS cc_start: 0.8347 (mmtp) cc_final: 0.7888 (mmtp) REVERT: C 191 LEU cc_start: 0.8610 (tp) cc_final: 0.8323 (tt) REVERT: C 199 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6394 (pp) REVERT: C 208 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 212 VAL cc_start: 0.8446 (t) cc_final: 0.8209 (p) REVERT: C 271 LEU cc_start: 0.8116 (mt) cc_final: 0.7727 (mm) REVERT: C 298 VAL cc_start: 0.8342 (m) cc_final: 0.8050 (p) REVERT: E 5 MET cc_start: 0.7188 (mpp) cc_final: 0.6949 (mmm) REVERT: E 172 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8126 (mp) REVERT: E 203 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5748 (pm20) REVERT: E 206 MET cc_start: 0.7910 (mtm) cc_final: 0.7402 (mtm) REVERT: E 318 MET cc_start: 0.8043 (tpp) cc_final: 0.7671 (tpp) REVERT: E 332 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8237 (mt) outliers start: 60 outliers final: 36 residues processed: 223 average time/residue: 0.0464 time to fit residues: 15.6901 Evaluate side-chains 238 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 TRP Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.0470 chunk 69 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101898 restraints weight = 9822.653| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.15 r_work: 0.3127 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6141 Z= 0.140 Angle : 0.527 6.616 8361 Z= 0.265 Chirality : 0.040 0.159 1014 Planarity : 0.004 0.041 990 Dihedral : 6.986 51.842 809 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 9.12 % Allowed : 25.31 % Favored : 65.57 % 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: 1.96 (0.33), residues: 738 helix: 2.10 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -2.80 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.008 0.001 TYR A 226 PHE 0.015 0.001 PHE E 27 TRP 0.012 0.001 TRP A 189 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6141) covalent geometry : angle 0.52654 ( 8361) hydrogen bonds : bond 0.03475 ( 444) hydrogen bonds : angle 3.77426 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 0.191 Fit side-chains REVERT: A 54 LYS cc_start: 0.8412 (mmtp) cc_final: 0.7935 (mmtp) REVERT: A 184 MET cc_start: 0.8397 (mmm) cc_final: 0.8036 (tpp) REVERT: A 203 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6340 (pm20) REVERT: A 208 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8217 (mm) REVERT: A 212 VAL cc_start: 0.8563 (t) cc_final: 0.8326 (p) REVERT: A 267 ILE cc_start: 0.8393 (mt) cc_final: 0.8175 (mm) REVERT: A 298 VAL cc_start: 0.8601 (t) cc_final: 0.8362 (p) REVERT: A 332 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8484 (mt) REVERT: A 334 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7110 (m-70) REVERT: C 54 LYS cc_start: 0.8417 (mmtp) cc_final: 0.7951 (mmtp) REVERT: C 191 LEU cc_start: 0.8670 (tp) cc_final: 0.8402 (tt) REVERT: C 208 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8060 (mm) REVERT: C 212 VAL cc_start: 0.8501 (t) cc_final: 0.8263 (p) REVERT: C 271 LEU cc_start: 0.8203 (mt) cc_final: 0.7825 (mm) REVERT: C 298 VAL cc_start: 0.8430 (m) cc_final: 0.8144 (p) REVERT: E 5 MET cc_start: 0.7223 (mpp) cc_final: 0.6980 (mmm) REVERT: E 172 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8227 (mp) REVERT: E 203 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5809 (pm20) REVERT: E 206 MET cc_start: 0.8086 (mtm) cc_final: 0.7568 (mtm) REVERT: E 332 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8299 (mt) outliers start: 58 outliers final: 37 residues processed: 226 average time/residue: 0.0484 time to fit residues: 16.5466 Evaluate side-chains 241 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 50 optimal weight: 0.0470 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103570 restraints weight = 9734.543| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.15 r_work: 0.3138 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6141 Z= 0.130 Angle : 0.524 6.588 8361 Z= 0.262 Chirality : 0.040 0.163 1014 Planarity : 0.004 0.041 990 Dihedral : 6.958 54.868 807 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 8.96 % Allowed : 25.47 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.33), residues: 738 helix: 2.14 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -2.80 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.007 0.001 TYR A 226 PHE 0.015 0.001 PHE E 27 TRP 0.013 0.001 TRP A 189 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6141) covalent geometry : angle 0.52413 ( 8361) hydrogen bonds : bond 0.03369 ( 444) hydrogen bonds : angle 3.73784 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.227 Fit side-chains REVERT: F 7 TRP cc_start: 0.7175 (OUTLIER) cc_final: 0.6943 (t60) REVERT: A 54 LYS cc_start: 0.8395 (mmtp) cc_final: 0.7926 (mmtp) REVERT: A 203 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6342 (pm20) REVERT: A 208 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8220 (mm) REVERT: A 212 VAL cc_start: 0.8555 (t) cc_final: 0.8328 (p) REVERT: A 298 VAL cc_start: 0.8543 (t) cc_final: 0.8326 (p) REVERT: A 332 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8362 (mt) REVERT: A 334 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.6866 (m90) REVERT: C 54 LYS cc_start: 0.8415 (mmtp) cc_final: 0.7952 (mmtp) REVERT: C 191 LEU cc_start: 0.8676 (tp) cc_final: 0.8410 (tt) REVERT: C 208 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8062 (mm) REVERT: C 212 VAL cc_start: 0.8500 (t) cc_final: 0.8259 (p) REVERT: C 271 LEU cc_start: 0.8198 (mt) cc_final: 0.7823 (mm) REVERT: C 298 VAL cc_start: 0.8423 (m) cc_final: 0.8153 (p) REVERT: E 5 MET cc_start: 0.7230 (mpp) cc_final: 0.6987 (mmm) REVERT: E 203 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5951 (pm20) REVERT: E 206 MET cc_start: 0.8098 (mtm) cc_final: 0.7596 (mtm) REVERT: E 332 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8323 (mt) outliers start: 57 outliers final: 38 residues processed: 224 average time/residue: 0.0454 time to fit residues: 15.4910 Evaluate side-chains 240 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 TRP Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103515 restraints weight = 9717.670| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.14 r_work: 0.3130 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6141 Z= 0.136 Angle : 0.524 6.578 8361 Z= 0.263 Chirality : 0.040 0.168 1014 Planarity : 0.004 0.043 990 Dihedral : 6.967 57.343 807 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 8.96 % Allowed : 25.00 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.33), residues: 738 helix: 2.15 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -2.77 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.007 0.001 TYR A 226 PHE 0.015 0.001 PHE E 27 TRP 0.012 0.001 TRP A 189 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6141) covalent geometry : angle 0.52393 ( 8361) hydrogen bonds : bond 0.03433 ( 444) hydrogen bonds : angle 3.73115 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.163 Fit side-chains REVERT: A 54 LYS cc_start: 0.8415 (mmtp) cc_final: 0.7944 (mmtp) REVERT: A 203 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6355 (pm20) REVERT: A 208 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 212 VAL cc_start: 0.8553 (t) cc_final: 0.8326 (p) REVERT: A 298 VAL cc_start: 0.8557 (t) cc_final: 0.8328 (p) REVERT: A 332 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 334 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.6890 (m90) REVERT: C 54 LYS cc_start: 0.8433 (mmtp) cc_final: 0.7968 (mmtp) REVERT: C 191 LEU cc_start: 0.8675 (tp) cc_final: 0.8404 (tt) REVERT: C 208 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8061 (mm) REVERT: C 212 VAL cc_start: 0.8475 (t) cc_final: 0.8232 (p) REVERT: C 271 LEU cc_start: 0.8212 (mt) cc_final: 0.7829 (mm) REVERT: C 298 VAL cc_start: 0.8446 (m) cc_final: 0.8157 (p) REVERT: E 5 MET cc_start: 0.7197 (mpp) cc_final: 0.6963 (mmm) REVERT: E 203 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5927 (pm20) REVERT: E 206 MET cc_start: 0.8111 (mtm) cc_final: 0.7602 (mtm) REVERT: E 280 LEU cc_start: 0.8150 (mm) cc_final: 0.7930 (mt) REVERT: E 332 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8320 (mt) outliers start: 57 outliers final: 40 residues processed: 224 average time/residue: 0.0361 time to fit residues: 12.3863 Evaluate side-chains 242 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103212 restraints weight = 9904.453| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.17 r_work: 0.3121 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6141 Z= 0.146 Angle : 0.542 6.572 8361 Z= 0.272 Chirality : 0.041 0.175 1014 Planarity : 0.004 0.039 990 Dihedral : 6.775 59.163 805 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 7.86 % Allowed : 26.26 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.33), residues: 738 helix: 2.14 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -2.77 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.006 0.001 TYR A 226 PHE 0.015 0.001 PHE E 27 TRP 0.029 0.002 TRP F 7 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6141) covalent geometry : angle 0.54183 ( 8361) hydrogen bonds : bond 0.03505 ( 444) hydrogen bonds : angle 3.75671 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.132 Fit side-chains REVERT: A 54 LYS cc_start: 0.8424 (mmtp) cc_final: 0.7955 (mmtp) REVERT: A 203 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6362 (pm20) REVERT: A 208 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 212 VAL cc_start: 0.8562 (t) cc_final: 0.8334 (p) REVERT: A 298 VAL cc_start: 0.8587 (t) cc_final: 0.8351 (p) REVERT: A 332 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8433 (mt) REVERT: A 334 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7054 (m-70) REVERT: C 54 LYS cc_start: 0.8432 (mmtp) cc_final: 0.7969 (mmtp) REVERT: C 191 LEU cc_start: 0.8678 (tp) cc_final: 0.8417 (tt) REVERT: C 208 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8058 (mm) REVERT: C 212 VAL cc_start: 0.8510 (t) cc_final: 0.8269 (p) REVERT: C 271 LEU cc_start: 0.8224 (mt) cc_final: 0.7847 (mm) REVERT: C 298 VAL cc_start: 0.8457 (m) cc_final: 0.8175 (p) REVERT: E 5 MET cc_start: 0.7198 (mpp) cc_final: 0.6963 (mmm) REVERT: E 203 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5716 (pm20) REVERT: E 206 MET cc_start: 0.8132 (mtm) cc_final: 0.7627 (mtm) REVERT: E 280 LEU cc_start: 0.8156 (mm) cc_final: 0.7942 (mt) REVERT: E 332 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8332 (mt) outliers start: 50 outliers final: 38 residues processed: 222 average time/residue: 0.0448 time to fit residues: 15.1035 Evaluate side-chains 238 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101958 restraints weight = 9891.868| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.21 r_work: 0.3109 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6141 Z= 0.161 Angle : 0.548 6.548 8361 Z= 0.277 Chirality : 0.041 0.173 1014 Planarity : 0.004 0.041 990 Dihedral : 6.779 58.311 805 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 7.70 % Allowed : 26.26 % Favored : 66.04 % 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: 1.98 (0.33), residues: 738 helix: 2.10 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -2.74 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.007 0.001 TYR A 226 PHE 0.015 0.001 PHE E 27 TRP 0.027 0.002 TRP F 7 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6141) covalent geometry : angle 0.54755 ( 8361) hydrogen bonds : bond 0.03659 ( 444) hydrogen bonds : angle 3.80964 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.226 Fit side-chains REVERT: A 54 LYS cc_start: 0.8320 (mmtp) cc_final: 0.7850 (mmtp) REVERT: A 203 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6225 (pm20) REVERT: A 208 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8150 (mm) REVERT: A 212 VAL cc_start: 0.8481 (t) cc_final: 0.8260 (p) REVERT: A 298 VAL cc_start: 0.8529 (t) cc_final: 0.8278 (p) REVERT: A 332 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 334 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7075 (m-70) REVERT: C 54 LYS cc_start: 0.8366 (mmtp) cc_final: 0.7912 (mmtp) REVERT: C 191 LEU cc_start: 0.8607 (tp) cc_final: 0.8356 (tt) REVERT: C 208 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7965 (mm) REVERT: C 212 VAL cc_start: 0.8445 (t) cc_final: 0.8197 (p) REVERT: C 271 LEU cc_start: 0.8145 (mt) cc_final: 0.7745 (mm) REVERT: C 298 VAL cc_start: 0.8392 (m) cc_final: 0.8106 (p) REVERT: E 5 MET cc_start: 0.7185 (mpp) cc_final: 0.6952 (mmm) REVERT: E 203 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5746 (pm20) REVERT: E 206 MET cc_start: 0.7978 (mtm) cc_final: 0.7456 (mtm) REVERT: E 280 LEU cc_start: 0.8153 (mm) cc_final: 0.7949 (mt) REVERT: E 332 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8276 (mt) outliers start: 49 outliers final: 36 residues processed: 220 average time/residue: 0.0444 time to fit residues: 14.8999 Evaluate side-chains 236 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain B residue 7 TRP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102659 restraints weight = 9842.090| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.20 r_work: 0.3115 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6141 Z= 0.153 Angle : 0.547 6.538 8361 Z= 0.275 Chirality : 0.041 0.174 1014 Planarity : 0.004 0.038 990 Dihedral : 6.486 52.197 803 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 7.23 % Allowed : 26.89 % Favored : 65.88 % 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: 1.97 (0.33), residues: 738 helix: 2.09 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -2.73 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.006 0.001 TYR A 226 PHE 0.016 0.001 PHE E 27 TRP 0.027 0.002 TRP F 7 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6141) covalent geometry : angle 0.54652 ( 8361) hydrogen bonds : bond 0.03596 ( 444) hydrogen bonds : angle 3.78895 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.23 seconds wall clock time: 25 minutes 5.63 seconds (1505.63 seconds total)