Starting phenix.real_space_refine on Thu Mar 5 08:44:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d45_27175/03_2026/8d45_27175.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d45_27175/03_2026/8d45_27175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d45_27175/03_2026/8d45_27175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d45_27175/03_2026/8d45_27175.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d45_27175/03_2026/8d45_27175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d45_27175/03_2026/8d45_27175.map" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 6716 2.51 5 N 1846 2.21 5 O 1944 1.98 5 H 10370 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20932 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "B" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "C" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "D" Number of atoms: 5257 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 5233 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 318} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 341, 5233 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 318} Chain breaks: 2 bond proxies already assigned to first conformer: 5272 Time building chain proxies: 6.19, per 1000 atoms: 0.30 Number of scatterers: 20932 At special positions: 0 Unit cell: (103.79, 63.13, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 1944 8.00 N 1846 7.00 C 6716 6.00 H 10370 1.00 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: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 54.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 96 through 113 removed outlier: 3.752A pdb=" N ASN A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 152 removed outlier: 3.906A pdb=" N VAL A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.700A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 220 through 239 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.853A pdb=" N ASP A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.739A pdb=" N ARG A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 332 through 338 removed outlier: 4.006A pdb=" N MET A 337 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 96 through 112 Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.871A pdb=" N VAL B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 3.535A pdb=" N ALA B 167 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 222 through 239 Processing helix chain 'B' and resid 277 through 292 removed outlier: 4.011A pdb=" N ARG B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.959A pdb=" N MET B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 348 through 355 removed outlier: 3.515A pdb=" N TRP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 19 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.708A pdb=" N GLU C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 96 through 113 removed outlier: 3.644A pdb=" N ASN C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 152 removed outlier: 3.902A pdb=" N VAL C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.659A pdb=" N ALA C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 209 Processing helix chain 'C' and resid 222 through 238 Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.000A pdb=" N ARG C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 322 through 328 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.536A pdb=" N ASP C 336 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 348 through 355 removed outlier: 3.574A pdb=" N TRP C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 52 through 67 Processing helix chain 'D' and resid 96 through 112 Processing helix chain 'D' and resid 134 through 152 removed outlier: 3.871A pdb=" N VAL D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 148 " --> pdb=" O GLN D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.557A pdb=" N ALA D 167 " --> pdb=" O HIS D 163 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 220 through 238 Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.845A pdb=" N ILE D 262 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP D 263 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 4.009A pdb=" N ARG D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.922A pdb=" N MET D 337 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 348 through 355 removed outlier: 3.697A pdb=" N TRP D 352 " --> pdb=" O ARG D 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 123 removed outlier: 5.833A pdb=" N VAL A 122 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 72 removed outlier: 3.569A pdb=" N ALA B 119 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 244 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.619A pdb=" N LEU C 156 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR C 184 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA C 158 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 70 through 72 518 hydrogen bonds defined for protein. 1440 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: 5.47 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 10342 1.02 - 1.22: 33 1.22 - 1.42: 4492 1.42 - 1.61: 6246 1.61 - 1.81: 84 Bond restraints: 21197 Sorted by residual: bond pdb=" NE ARG B 108 " pdb=" HE ARG B 108 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C TRP B 44 " pdb=" N THR B 45 " ideal model delta sigma weight residual 1.331 1.384 -0.053 2.07e-02 2.33e+03 6.62e+00 bond pdb=" C TRP C 44 " pdb=" N THR C 45 " ideal model delta sigma weight residual 1.331 1.378 -0.047 2.07e-02 2.33e+03 5.09e+00 bond pdb=" N THR B 222 " pdb=" CA THR B 222 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.25e-02 6.40e+03 4.23e+00 bond pdb=" N THR C 222 " pdb=" CA THR C 222 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.27e-02 6.20e+03 3.26e+00 ... (remaining 21192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 36595 1.47 - 2.94: 1590 2.94 - 4.41: 173 4.41 - 5.88: 31 5.88 - 7.35: 3 Bond angle restraints: 38392 Sorted by residual: angle pdb=" CG LYS A 139 " pdb=" CD LYS A 139 " pdb=" CE LYS A 139 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N ASN A 152 " pdb=" CA ASN A 152 " pdb=" C ASN A 152 " ideal model delta sigma weight residual 110.91 107.56 3.35 1.17e+00 7.31e-01 8.18e+00 angle pdb=" N ARG A 239 " pdb=" CA ARG A 239 " pdb=" C ARG A 239 " ideal model delta sigma weight residual 111.24 107.32 3.92 1.38e+00 5.25e-01 8.09e+00 angle pdb=" N ARG B 239 " pdb=" CA ARG B 239 " pdb=" C ARG B 239 " ideal model delta sigma weight residual 111.24 107.40 3.84 1.38e+00 5.25e-01 7.74e+00 angle pdb=" N ASN C 152 " pdb=" CA ASN C 152 " pdb=" C ASN C 152 " ideal model delta sigma weight residual 110.91 107.68 3.23 1.17e+00 7.31e-01 7.63e+00 ... (remaining 38387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8644 17.62 - 35.24: 929 35.24 - 52.87: 323 52.87 - 70.49: 83 70.49 - 88.11: 27 Dihedral angle restraints: 10006 sinusoidal: 5439 harmonic: 4567 Sorted by residual: dihedral pdb=" CA ASP C 336 " pdb=" C ASP C 336 " pdb=" N MET C 337 " pdb=" CA MET C 337 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE C 74 " pdb=" C PHE C 74 " pdb=" N THR C 75 " pdb=" CA THR C 75 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE D 74 " pdb=" C PHE D 74 " pdb=" N THR D 75 " pdb=" CA THR D 75 " ideal model delta harmonic sigma weight residual 180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 10003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 853 0.029 - 0.058: 422 0.058 - 0.087: 176 0.087 - 0.115: 80 0.115 - 0.144: 23 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA PRO A 46 " pdb=" N PRO A 46 " pdb=" C PRO A 46 " pdb=" CB PRO A 46 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA PRO B 46 " pdb=" N PRO B 46 " pdb=" C PRO B 46 " pdb=" CB PRO B 46 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL A 196 " pdb=" N VAL A 196 " pdb=" C VAL A 196 " pdb=" CB VAL A 196 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1551 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 109 " -0.077 2.00e-02 2.50e+03 8.49e-02 1.08e+02 pdb=" CD GLN B 109 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN B 109 " 0.077 2.00e-02 2.50e+03 pdb=" NE2 GLN B 109 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN B 109 " 0.125 2.00e-02 2.50e+03 pdb="HE22 GLN B 109 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 315 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D 316 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 316 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 316 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 315 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO C 316 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 316 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 316 " -0.040 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1588 2.21 - 2.81: 45468 2.81 - 3.41: 62571 3.41 - 4.00: 84710 4.00 - 4.60: 129854 Nonbonded interactions: 324191 Sorted by model distance: nonbonded pdb=" H ALA C 158 " pdb=" O ALA C 182 " model vdw 1.613 2.450 nonbonded pdb=" O ALA C 158 " pdb=" H THR C 184 " model vdw 1.626 2.450 nonbonded pdb=" O ILE D 24 " pdb=" H ASN D 69 " model vdw 1.686 2.450 nonbonded pdb=" O ILE A 357 " pdb="HD22 ASN B 364 " model vdw 1.686 2.450 nonbonded pdb=" O ILE B 24 " pdb=" H ASN B 69 " model vdw 1.700 2.450 ... (remaining 324186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'B' and (resid 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'C' and (resid 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'D' and (resid 9 through 14 or resid 16 through 127 or resid 134 through \ 325 or resid 327 through 372)) } 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=0.40 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.660 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10827 Z= 0.201 Angle : 0.788 7.348 14666 Z= 0.445 Chirality : 0.044 0.144 1554 Planarity : 0.007 0.072 1935 Dihedral : 17.508 88.110 4022 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.92 % Allowed : 18.26 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.43 (0.22), residues: 1342 helix: -0.69 (0.19), residues: 676 sheet: -1.97 (0.32), residues: 132 loop : -0.76 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 356 TYR 0.016 0.002 TYR C 295 PHE 0.034 0.003 PHE B 155 TRP 0.011 0.001 TRP B 342 HIS 0.007 0.002 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00427 (10827) covalent geometry : angle 0.78810 (14666) hydrogen bonds : bond 0.19437 ( 518) hydrogen bonds : angle 7.46816 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 MET cc_start: 0.7725 (mmt) cc_final: 0.7139 (mmt) outliers start: 8 outliers final: 7 residues processed: 145 average time/residue: 0.9596 time to fit residues: 153.5687 Evaluate side-chains 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 186 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 290 ASN B 152 ASN B 290 ASN C 152 ASN C 354 ASN D 152 ASN D 290 ASN D 354 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.180087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139840 restraints weight = 61810.457| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.93 r_work: 0.3638 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10827 Z= 0.181 Angle : 0.652 5.287 14666 Z= 0.342 Chirality : 0.042 0.146 1554 Planarity : 0.007 0.061 1935 Dihedral : 5.108 41.808 1483 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.39 % Allowed : 16.42 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.22), residues: 1342 helix: -0.35 (0.19), residues: 678 sheet: -2.17 (0.33), residues: 130 loop : -0.65 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 348 TYR 0.015 0.002 TYR B 295 PHE 0.012 0.002 PHE D 141 TRP 0.008 0.001 TRP B 342 HIS 0.008 0.002 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00413 (10827) covalent geometry : angle 0.65220 (14666) hydrogen bonds : bond 0.05282 ( 518) hydrogen bonds : angle 5.92015 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.5733 (t80) REVERT: B 31 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7134 (t80) REVERT: C 31 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.5994 (t80) REVERT: C 149 MET cc_start: 0.7293 (mmm) cc_final: 0.6988 (mmp) REVERT: D 31 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6010 (t80) REVERT: D 71 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.5899 (mpt) outliers start: 24 outliers final: 8 residues processed: 138 average time/residue: 0.9898 time to fit residues: 150.1610 Evaluate side-chains 134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.178530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138125 restraints weight = 61293.074| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.63 r_work: 0.3623 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10827 Z= 0.217 Angle : 0.661 4.902 14666 Z= 0.345 Chirality : 0.044 0.150 1554 Planarity : 0.007 0.054 1935 Dihedral : 4.814 28.141 1477 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.94 % Allowed : 15.60 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.00 (0.22), residues: 1342 helix: -0.14 (0.20), residues: 651 sheet: -2.15 (0.33), residues: 133 loop : -0.73 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 278 TYR 0.023 0.003 TYR B 295 PHE 0.013 0.002 PHE B 148 TRP 0.010 0.001 TRP D 279 HIS 0.008 0.002 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00503 (10827) covalent geometry : angle 0.66142 (14666) hydrogen bonds : bond 0.05115 ( 518) hydrogen bonds : angle 5.69153 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6018 (t80) REVERT: B 31 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6949 (t80) REVERT: B 356 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7476 (tpt170) REVERT: C 31 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.6140 (t80) REVERT: C 149 MET cc_start: 0.7283 (mmm) cc_final: 0.7046 (mmp) REVERT: D 31 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.6614 (t80) outliers start: 30 outliers final: 11 residues processed: 144 average time/residue: 1.0664 time to fit residues: 168.3989 Evaluate side-chains 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 354 ASN C 152 ASN C 163 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.180254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140238 restraints weight = 62674.933| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 3.70 r_work: 0.3640 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10827 Z= 0.155 Angle : 0.606 5.018 14666 Z= 0.313 Chirality : 0.042 0.141 1554 Planarity : 0.006 0.087 1935 Dihedral : 4.618 26.478 1477 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.29 % Allowed : 16.15 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1342 helix: 0.28 (0.20), residues: 635 sheet: -2.16 (0.34), residues: 133 loop : -0.41 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 308 TYR 0.017 0.002 TYR B 295 PHE 0.014 0.002 PHE D 261 TRP 0.011 0.001 TRP D 279 HIS 0.006 0.002 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00360 (10827) covalent geometry : angle 0.60625 (14666) hydrogen bonds : bond 0.04522 ( 518) hydrogen bonds : angle 5.50503 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.5950 (t80) REVERT: B 31 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6903 (t80) REVERT: B 356 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7455 (tpt170) REVERT: C 31 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6137 (t80) REVERT: C 149 MET cc_start: 0.7275 (mmm) cc_final: 0.7052 (mmp) REVERT: C 213 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7031 (mm) REVERT: D 31 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6602 (t80) REVERT: D 71 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.5573 (mpm) outliers start: 23 outliers final: 9 residues processed: 139 average time/residue: 0.9928 time to fit residues: 151.8941 Evaluate side-chains 136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 245 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN C 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.179521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.140076 restraints weight = 57922.830| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 3.37 r_work: 0.3653 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10827 Z= 0.154 Angle : 0.591 4.925 14666 Z= 0.304 Chirality : 0.042 0.139 1554 Planarity : 0.006 0.075 1935 Dihedral : 4.466 26.068 1477 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.03 % Allowed : 16.06 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.23), residues: 1342 helix: 0.53 (0.20), residues: 633 sheet: -2.23 (0.34), residues: 133 loop : -0.30 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 308 TYR 0.017 0.002 TYR B 295 PHE 0.013 0.002 PHE D 141 TRP 0.009 0.001 TRP D 279 HIS 0.006 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00359 (10827) covalent geometry : angle 0.59102 (14666) hydrogen bonds : bond 0.04363 ( 518) hydrogen bonds : angle 5.36453 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6027 (t80) REVERT: A 337 MET cc_start: 0.5215 (ptp) cc_final: 0.4374 (ptm) REVERT: B 31 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.6882 (t80) REVERT: B 148 PHE cc_start: 0.7264 (m-80) cc_final: 0.6973 (m-80) REVERT: B 149 MET cc_start: 0.7214 (mmm) cc_final: 0.7012 (mmp) REVERT: B 284 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7357 (t80) REVERT: B 356 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7568 (tpt170) REVERT: C 31 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6260 (t80) REVERT: C 124 GLN cc_start: 0.7044 (tt0) cc_final: 0.6784 (tp40) REVERT: D 31 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.6726 (t80) REVERT: D 51 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6357 (mt-10) REVERT: D 71 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.5621 (mpm) REVERT: D 337 MET cc_start: 0.4518 (ppp) cc_final: 0.4171 (ppp) outliers start: 31 outliers final: 10 residues processed: 144 average time/residue: 0.9481 time to fit residues: 150.9205 Evaluate side-chains 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 245 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN C 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.179475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140339 restraints weight = 58930.307| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.64 r_work: 0.3647 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10827 Z= 0.151 Angle : 0.586 5.394 14666 Z= 0.301 Chirality : 0.042 0.140 1554 Planarity : 0.005 0.083 1935 Dihedral : 4.402 25.784 1477 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.66 % Allowed : 16.70 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1342 helix: 0.65 (0.20), residues: 633 sheet: -2.12 (0.34), residues: 127 loop : -0.21 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 308 TYR 0.017 0.002 TYR B 295 PHE 0.033 0.002 PHE A 155 TRP 0.009 0.001 TRP D 279 HIS 0.006 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00353 (10827) covalent geometry : angle 0.58601 (14666) hydrogen bonds : bond 0.04280 ( 518) hydrogen bonds : angle 5.28900 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6014 (t80) REVERT: A 337 MET cc_start: 0.5181 (ptp) cc_final: 0.4388 (ptm) REVERT: B 30 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8335 (t) REVERT: B 31 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6839 (t80) REVERT: B 148 PHE cc_start: 0.7217 (m-80) cc_final: 0.6961 (m-80) REVERT: B 149 MET cc_start: 0.7169 (mmm) cc_final: 0.6954 (mmp) REVERT: B 284 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7410 (t80) REVERT: B 356 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7383 (tpt170) REVERT: C 31 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6296 (t80) REVERT: C 231 MET cc_start: 0.7348 (mtt) cc_final: 0.7118 (mtt) REVERT: C 284 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7428 (t80) REVERT: D 31 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6748 (t80) REVERT: D 51 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6336 (mt-10) REVERT: D 71 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.5476 (mpm) REVERT: D 284 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7294 (t80) REVERT: D 337 MET cc_start: 0.4760 (ppp) cc_final: 0.4440 (ppp) outliers start: 27 outliers final: 10 residues processed: 139 average time/residue: 0.9865 time to fit residues: 150.7713 Evaluate side-chains 139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 284 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 31 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.179697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139905 restraints weight = 63518.842| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.75 r_work: 0.3635 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10827 Z= 0.151 Angle : 0.587 5.646 14666 Z= 0.302 Chirality : 0.042 0.138 1554 Planarity : 0.005 0.081 1935 Dihedral : 4.377 25.529 1477 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.57 % Allowed : 17.06 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1342 helix: 0.72 (0.20), residues: 633 sheet: -2.34 (0.33), residues: 133 loop : -0.22 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 308 TYR 0.018 0.002 TYR C 295 PHE 0.024 0.002 PHE A 155 TRP 0.009 0.001 TRP D 279 HIS 0.006 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00352 (10827) covalent geometry : angle 0.58718 (14666) hydrogen bonds : bond 0.04249 ( 518) hydrogen bonds : angle 5.26075 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6163 (t80) REVERT: A 51 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6224 (mt-10) REVERT: A 337 MET cc_start: 0.5186 (ptp) cc_final: 0.4429 (ptm) REVERT: B 31 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6865 (t80) REVERT: B 148 PHE cc_start: 0.7257 (m-80) cc_final: 0.6972 (m-80) REVERT: B 149 MET cc_start: 0.7222 (mmm) cc_final: 0.6954 (mmp) REVERT: B 284 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.7421 (t80) REVERT: B 356 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7402 (tpt170) REVERT: C 31 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.6393 (t80) REVERT: C 231 MET cc_start: 0.7445 (mtt) cc_final: 0.7210 (mtt) REVERT: D 31 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6776 (t80) REVERT: D 51 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6360 (mt-10) REVERT: D 71 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.5512 (mpm) REVERT: D 284 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.7340 (t80) REVERT: D 337 MET cc_start: 0.4760 (ppp) cc_final: 0.4441 (ppp) outliers start: 26 outliers final: 7 residues processed: 138 average time/residue: 1.0094 time to fit residues: 153.6313 Evaluate side-chains 135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 284 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 74 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 152 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 163 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.179035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140459 restraints weight = 52300.111| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.74 r_work: 0.3681 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10827 Z= 0.172 Angle : 0.604 6.043 14666 Z= 0.311 Chirality : 0.042 0.144 1554 Planarity : 0.006 0.081 1935 Dihedral : 4.406 25.045 1476 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.39 % Allowed : 17.25 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.23), residues: 1342 helix: 0.62 (0.20), residues: 635 sheet: -2.40 (0.32), residues: 133 loop : -0.31 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 308 TYR 0.020 0.002 TYR B 295 PHE 0.024 0.002 PHE A 155 TRP 0.008 0.001 TRP D 279 HIS 0.007 0.002 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00403 (10827) covalent geometry : angle 0.60432 (14666) hydrogen bonds : bond 0.04385 ( 518) hydrogen bonds : angle 5.27395 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6352 (t80) REVERT: A 51 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6211 (mt-10) REVERT: A 152 ASN cc_start: 0.7197 (OUTLIER) cc_final: 0.6953 (t0) REVERT: A 337 MET cc_start: 0.5219 (ptp) cc_final: 0.4414 (ptm) REVERT: B 31 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 51 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6593 (mt-10) REVERT: B 148 PHE cc_start: 0.7280 (m-80) cc_final: 0.6952 (m-80) REVERT: B 356 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7535 (tpt170) REVERT: C 31 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6518 (t80) REVERT: C 231 MET cc_start: 0.7435 (mtt) cc_final: 0.7212 (mtt) REVERT: D 31 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.6808 (t80) REVERT: D 51 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6399 (mt-10) REVERT: D 71 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.5600 (mpm) REVERT: D 337 MET cc_start: 0.4832 (ppp) cc_final: 0.4481 (ppp) outliers start: 24 outliers final: 8 residues processed: 134 average time/residue: 1.0381 time to fit residues: 152.5771 Evaluate side-chains 136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 92 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.179242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139716 restraints weight = 59090.440| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.40 r_work: 0.3632 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 10827 Z= 0.206 Angle : 0.862 59.187 14666 Z= 0.507 Chirality : 0.044 0.499 1554 Planarity : 0.006 0.082 1935 Dihedral : 4.410 25.034 1476 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.02 % Allowed : 17.43 % Favored : 80.55 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1342 helix: 0.63 (0.20), residues: 635 sheet: -2.42 (0.32), residues: 133 loop : -0.32 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 308 TYR 0.017 0.002 TYR B 295 PHE 0.022 0.002 PHE A 155 TRP 0.008 0.001 TRP D 279 HIS 0.006 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00461 (10827) covalent geometry : angle 0.86193 (14666) hydrogen bonds : bond 0.04367 ( 518) hydrogen bonds : angle 5.26890 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6314 (t80) REVERT: A 51 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.6169 (mt-10) REVERT: A 337 MET cc_start: 0.5217 (ptp) cc_final: 0.4462 (ptm) REVERT: B 31 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6788 (t80) REVERT: B 51 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: B 148 PHE cc_start: 0.7258 (m-80) cc_final: 0.6972 (m-80) REVERT: B 356 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7388 (tpt170) REVERT: C 31 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.6485 (t80) REVERT: C 231 MET cc_start: 0.7349 (mtt) cc_final: 0.7120 (mtt) REVERT: D 31 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6787 (t80) REVERT: D 51 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6385 (mt-10) REVERT: D 71 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.5521 (mpm) REVERT: D 337 MET cc_start: 0.4872 (ppp) cc_final: 0.4515 (ppp) outliers start: 20 outliers final: 8 residues processed: 129 average time/residue: 1.0549 time to fit residues: 149.0379 Evaluate side-chains 133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.0370 chunk 114 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.179205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139997 restraints weight = 59430.448| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.40 r_work: 0.3636 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 10827 Z= 0.205 Angle : 0.862 59.198 14666 Z= 0.507 Chirality : 0.044 0.498 1554 Planarity : 0.006 0.082 1935 Dihedral : 4.410 25.034 1476 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.83 % Allowed : 17.71 % Favored : 80.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1342 helix: 0.63 (0.20), residues: 635 sheet: -2.42 (0.32), residues: 133 loop : -0.32 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 308 TYR 0.017 0.002 TYR B 295 PHE 0.022 0.002 PHE A 155 TRP 0.008 0.001 TRP D 279 HIS 0.006 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00461 (10827) covalent geometry : angle 0.86194 (14666) hydrogen bonds : bond 0.04367 ( 518) hydrogen bonds : angle 5.26889 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6329 (t80) REVERT: A 51 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6185 (mt-10) REVERT: A 337 MET cc_start: 0.5217 (ptp) cc_final: 0.4463 (ptm) REVERT: B 31 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.6793 (t80) REVERT: B 51 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6558 (mt-10) REVERT: B 148 PHE cc_start: 0.7277 (m-80) cc_final: 0.6985 (m-80) REVERT: B 356 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7398 (tpt170) REVERT: C 31 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6499 (t80) REVERT: C 231 MET cc_start: 0.7360 (mtt) cc_final: 0.7130 (mtt) REVERT: D 31 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6794 (t80) REVERT: D 51 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6399 (mt-10) REVERT: D 71 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.5520 (mpm) REVERT: D 337 MET cc_start: 0.4872 (ppp) cc_final: 0.4517 (ppp) outliers start: 18 outliers final: 8 residues processed: 125 average time/residue: 1.0914 time to fit residues: 149.4815 Evaluate side-chains 133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.179204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140135 restraints weight = 57663.706| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.25 r_work: 0.3655 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 10827 Z= 0.205 Angle : 0.862 59.200 14666 Z= 0.507 Chirality : 0.044 0.498 1554 Planarity : 0.006 0.082 1935 Dihedral : 4.410 25.034 1476 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.83 % Allowed : 17.71 % Favored : 80.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1342 helix: 0.63 (0.20), residues: 635 sheet: -2.42 (0.32), residues: 133 loop : -0.32 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 308 TYR 0.017 0.002 TYR B 295 PHE 0.022 0.002 PHE A 155 TRP 0.008 0.001 TRP D 279 HIS 0.006 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00461 (10827) covalent geometry : angle 0.86194 (14666) hydrogen bonds : bond 0.04367 ( 518) hydrogen bonds : angle 5.26889 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8527.52 seconds wall clock time: 144 minutes 27.69 seconds (8667.69 seconds total)