Starting phenix.real_space_refine on Tue Mar 3 18:40:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v9m_31825/03_2026/7v9m_31825.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9m_31825/03_2026/7v9m_31825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v9m_31825/03_2026/7v9m_31825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9m_31825/03_2026/7v9m_31825.map" model { file = "/net/cci-nas-00/data/ceres_data/7v9m_31825/03_2026/7v9m_31825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9m_31825/03_2026/7v9m_31825.cif" } resolution = 3.29 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= 0.022 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 45 5.16 5 C 5167 2.51 5 N 1419 2.21 5 O 1507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 8138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1867 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2125 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 1.69, per 1000 atoms: 0.21 Number of scatterers: 8138 At special positions: 0 Unit cell: (81.12, 98.8, 134.16, 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 45 16.00 O 1507 8.00 N 1419 7.00 C 5167 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: 0.84 Conformation dependent library (CDL) restraints added in 247.2 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.1% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.464A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.520A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.842A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.628A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 19 Processing helix chain 'R' and resid 56 through 90 removed outlier: 3.715A pdb=" N SER R 60 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS R 73 " --> pdb=" O TYR R 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 94 Processing helix chain 'R' and resid 95 through 122 Processing helix chain 'R' and resid 135 through 169 Processing helix chain 'R' and resid 174 through 202 removed outlier: 3.654A pdb=" N TRP R 179 " --> pdb=" O ARG R 175 " (cutoff:3.500A) Proline residue: R 189 - end of helix Processing helix chain 'R' and resid 206 through 210 removed outlier: 3.651A pdb=" N ASP R 210 " --> pdb=" O ALA R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 247 removed outlier: 3.901A pdb=" N TRP R 218 " --> pdb=" O THR R 214 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE R 221 " --> pdb=" O TYR R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix Processing helix chain 'R' and resid 259 through 274 removed outlier: 3.951A pdb=" N LEU R 263 " --> pdb=" O GLN R 259 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 275 through 277 No H-bonds generated for 'chain 'R' and resid 275 through 277' Processing helix chain 'R' and resid 278 through 283 removed outlier: 4.479A pdb=" N PHE R 283 " --> pdb=" O ILE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 313 Proline residue: R 295 - end of helix removed outlier: 3.677A pdb=" N PHE R 303 " --> pdb=" O GLY R 299 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY R 305 " --> pdb=" O GLY R 301 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 328 Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.716A pdb=" N GLN Y 11 " --> pdb=" O ALA Y 7 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 45 removed outlier: 3.687A pdb=" N ALA Y 43 " --> pdb=" O ALA Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.916A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.327A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.788A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.768A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.673A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.634A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.548A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.703A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.576A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2664 1.34 - 1.46: 1704 1.46 - 1.58: 3881 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 8309 Sorted by residual: bond pdb=" CG LEU B 190 " pdb=" CD1 LEU B 190 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.53e+00 bond pdb=" CB ILE R 109 " pdb=" CG2 ILE R 109 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 bond pdb=" CG LEU R 80 " pdb=" CD2 LEU R 80 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 bond pdb=" CB VAL R 65 " pdb=" CG2 VAL R 65 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.11e-01 bond pdb=" CB ASN R 232 " pdb=" CG ASN R 232 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.58e-01 ... (remaining 8304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 10824 1.48 - 2.96: 355 2.96 - 4.44: 62 4.44 - 5.91: 12 5.91 - 7.39: 2 Bond angle restraints: 11255 Sorted by residual: angle pdb=" N THR B 87 " pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 113.65 108.87 4.78 1.47e+00 4.63e-01 1.06e+01 angle pdb=" CA TRP A 234 " pdb=" CB TRP A 234 " pdb=" CG TRP A 234 " ideal model delta sigma weight residual 113.60 119.29 -5.69 1.90e+00 2.77e-01 8.96e+00 angle pdb=" C SER N 112 " pdb=" N THR N 113 " pdb=" CA THR N 113 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.84e+00 angle pdb=" N VAL B 187 " pdb=" CA VAL B 187 " pdb=" C VAL B 187 " ideal model delta sigma weight residual 106.21 109.06 -2.85 1.07e+00 8.73e-01 7.07e+00 angle pdb=" C GLY R 185 " pdb=" N TRP R 186 " pdb=" CA TRP R 186 " ideal model delta sigma weight residual 121.64 116.13 5.51 2.13e+00 2.20e-01 6.70e+00 ... (remaining 11250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4549 17.78 - 35.57: 303 35.57 - 53.35: 37 53.35 - 71.14: 14 71.14 - 88.92: 10 Dihedral angle restraints: 4913 sinusoidal: 1928 harmonic: 2985 Sorted by residual: dihedral pdb=" CA GLY B 162 " pdb=" C GLY B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA THR N 114 " pdb=" C THR N 114 " pdb=" N TYR N 115 " pdb=" CA TYR N 115 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 4910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 839 0.042 - 0.083: 326 0.083 - 0.125: 84 0.125 - 0.167: 11 0.167 - 0.208: 3 Chirality restraints: 1263 Sorted by residual: chirality pdb=" CB ILE R 109 " pdb=" CA ILE R 109 " pdb=" CG1 ILE R 109 " pdb=" CG2 ILE R 109 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TRP R 155 " pdb=" N TRP R 155 " pdb=" C TRP R 155 " pdb=" CB TRP R 155 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA TRP A 234 " pdb=" N TRP A 234 " pdb=" C TRP A 234 " pdb=" CB TRP A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1260 not shown) Planarity restraints: 1433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 295 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO R 295 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO R 295 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU R 296 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 297 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLU R 297 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU R 297 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU R 298 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 67 " 0.062 9.50e-02 1.11e+02 3.66e-02 7.51e+00 pdb=" NE ARG N 67 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG N 67 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG N 67 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG N 67 " -0.013 2.00e-02 2.50e+03 ... (remaining 1430 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 599 2.74 - 3.28: 8493 3.28 - 3.82: 13576 3.82 - 4.36: 16288 4.36 - 4.90: 28315 Nonbonded interactions: 67271 Sorted by model distance: nonbonded pdb=" OG1 THR A 364 " pdb=" OD1 ASN A 371 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR A 55 " pdb=" ND2 ASN A 292 " model vdw 2.205 3.120 nonbonded pdb=" NH2 ARG N 67 " pdb=" OD2 ASP N 90 " model vdw 2.208 3.120 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG B 8 " pdb=" OE1 GLN N 120 " model vdw 2.271 3.120 ... (remaining 67266 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.050 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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 0.046 8309 Z= 0.191 Angle : 0.655 7.392 11255 Z= 0.386 Chirality : 0.046 0.208 1263 Planarity : 0.006 0.077 1433 Dihedral : 13.185 88.919 2979 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.23 % Allowed : 3.99 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.26), residues: 1007 helix: 0.03 (0.24), residues: 387 sheet: 0.64 (0.36), residues: 226 loop : -0.81 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.006 ARG N 67 TYR 0.028 0.003 TYR R 69 PHE 0.025 0.002 PHE R 306 TRP 0.037 0.003 TRP A 234 HIS 0.005 0.001 HIS R 124 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8309) covalent geometry : angle 0.65497 (11255) hydrogen bonds : bond 0.13847 ( 425) hydrogen bonds : angle 6.56590 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7871 (tptp) cc_final: 0.7625 (tptp) REVERT: A 222 PHE cc_start: 0.7204 (m-80) cc_final: 0.6626 (m-80) REVERT: A 233 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7949 (mmmt) REVERT: A 265 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6877 (mtt180) REVERT: A 346 LEU cc_start: 0.8459 (mp) cc_final: 0.8245 (mt) REVERT: A 350 THR cc_start: 0.8534 (m) cc_final: 0.8296 (p) REVERT: A 392 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6839 (mm-30) REVERT: B 57 LYS cc_start: 0.7785 (pttm) cc_final: 0.7223 (pttm) REVERT: B 61 MET cc_start: 0.6441 (ppp) cc_final: 0.6133 (ppp) REVERT: B 95 LEU cc_start: 0.7648 (mt) cc_final: 0.7374 (mt) REVERT: B 118 ASP cc_start: 0.6522 (p0) cc_final: 0.6233 (p0) REVERT: B 119 ASN cc_start: 0.7614 (m-40) cc_final: 0.7371 (m-40) REVERT: B 135 VAL cc_start: 0.8174 (t) cc_final: 0.7889 (m) REVERT: B 137 ARG cc_start: 0.6827 (tpp-160) cc_final: 0.6540 (tpp-160) REVERT: B 187 VAL cc_start: 0.8104 (m) cc_final: 0.7732 (t) REVERT: B 189 SER cc_start: 0.7735 (p) cc_final: 0.7489 (t) REVERT: B 250 CYS cc_start: 0.7647 (m) cc_final: 0.7371 (m) REVERT: B 263 THR cc_start: 0.7836 (m) cc_final: 0.7524 (p) REVERT: B 298 ASP cc_start: 0.7284 (t0) cc_final: 0.6928 (t0) REVERT: B 300 LEU cc_start: 0.8101 (mt) cc_final: 0.7711 (mp) REVERT: B 333 ASP cc_start: 0.6763 (p0) cc_final: 0.6394 (p0) REVERT: N 32 TYR cc_start: 0.7346 (m-80) cc_final: 0.7110 (m-80) REVERT: R 106 THR cc_start: 0.7621 (p) cc_final: 0.7414 (t) REVERT: R 154 SER cc_start: 0.7802 (t) cc_final: 0.7601 (t) REVERT: R 231 VAL cc_start: 0.7613 (m) cc_final: 0.7403 (p) REVERT: R 268 LEU cc_start: 0.8022 (mt) cc_final: 0.7818 (mm) REVERT: R 279 ILE cc_start: 0.8014 (tp) cc_final: 0.7701 (tp) REVERT: R 290 LEU cc_start: 0.7419 (mp) cc_final: 0.7216 (mm) outliers start: 2 outliers final: 1 residues processed: 230 average time/residue: 0.1244 time to fit residues: 35.9045 Evaluate side-chains 199 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 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 31 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125919 restraints weight = 11465.405| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.10 r_work: 0.3482 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8309 Z= 0.153 Angle : 0.601 8.229 11255 Z= 0.327 Chirality : 0.044 0.173 1263 Planarity : 0.004 0.039 1433 Dihedral : 6.061 69.225 1118 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.05 % Allowed : 11.40 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1007 helix: 1.11 (0.25), residues: 383 sheet: 0.36 (0.34), residues: 225 loop : -0.80 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.018 0.002 TYR R 69 PHE 0.022 0.002 PHE R 306 TRP 0.020 0.002 TRP A 234 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8309) covalent geometry : angle 0.60115 (11255) hydrogen bonds : bond 0.04534 ( 425) hydrogen bonds : angle 5.00529 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8271 (tptp) cc_final: 0.7946 (tptp) REVERT: A 220 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6526 (t70) REVERT: A 222 PHE cc_start: 0.7552 (m-80) cc_final: 0.6519 (m-80) REVERT: A 230 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7805 (mt-10) REVERT: A 346 LEU cc_start: 0.8460 (mp) cc_final: 0.8206 (mm) REVERT: A 347 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7725 (ttp80) REVERT: A 350 THR cc_start: 0.8595 (m) cc_final: 0.8309 (p) REVERT: A 392 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 46 ARG cc_start: 0.6597 (mpp-170) cc_final: 0.6344 (mpp-170) REVERT: B 57 LYS cc_start: 0.8457 (pttm) cc_final: 0.8207 (pttm) REVERT: B 75 GLN cc_start: 0.7913 (mt0) cc_final: 0.7559 (mt0) REVERT: B 95 LEU cc_start: 0.7772 (mt) cc_final: 0.7507 (mt) REVERT: B 118 ASP cc_start: 0.7189 (p0) cc_final: 0.6804 (p0) REVERT: B 134 ARG cc_start: 0.7393 (ptt90) cc_final: 0.7179 (ptt90) REVERT: B 135 VAL cc_start: 0.8141 (t) cc_final: 0.7771 (m) REVERT: B 165 THR cc_start: 0.8199 (p) cc_final: 0.7852 (t) REVERT: B 197 ARG cc_start: 0.7476 (mtp180) cc_final: 0.6878 (mtp180) REVERT: B 219 ARG cc_start: 0.8291 (tpp80) cc_final: 0.7878 (mmt90) REVERT: B 263 THR cc_start: 0.8072 (m) cc_final: 0.7840 (p) REVERT: B 300 LEU cc_start: 0.8126 (mt) cc_final: 0.7808 (mp) REVERT: B 333 ASP cc_start: 0.7496 (p0) cc_final: 0.7230 (p0) REVERT: P 11 ARG cc_start: 0.7554 (ttm170) cc_final: 0.7067 (ttm170) REVERT: R 109 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8347 (mt) REVERT: R 181 LEU cc_start: 0.8135 (tp) cc_final: 0.7906 (tp) REVERT: R 231 VAL cc_start: 0.7882 (m) cc_final: 0.7678 (p) REVERT: R 279 ILE cc_start: 0.8161 (tp) cc_final: 0.7807 (tp) outliers start: 18 outliers final: 12 residues processed: 201 average time/residue: 0.1211 time to fit residues: 30.7860 Evaluate side-chains 205 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124035 restraints weight = 11218.821| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.17 r_work: 0.3464 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8309 Z= 0.177 Angle : 0.574 7.877 11255 Z= 0.312 Chirality : 0.044 0.175 1263 Planarity : 0.004 0.046 1433 Dihedral : 5.716 61.398 1118 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.96 % Allowed : 14.48 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1007 helix: 1.38 (0.26), residues: 383 sheet: 0.18 (0.34), residues: 225 loop : -0.91 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.019 0.002 TYR R 69 PHE 0.021 0.002 PHE R 306 TRP 0.019 0.002 TRP N 47 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8309) covalent geometry : angle 0.57419 (11255) hydrogen bonds : bond 0.04453 ( 425) hydrogen bonds : angle 4.82356 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8310 (tptp) cc_final: 0.7957 (tptp) REVERT: A 220 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6404 (t70) REVERT: A 222 PHE cc_start: 0.7491 (m-80) cc_final: 0.6283 (m-80) REVERT: A 230 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 346 LEU cc_start: 0.8263 (mp) cc_final: 0.8039 (mm) REVERT: A 350 THR cc_start: 0.8451 (m) cc_final: 0.8179 (p) REVERT: A 378 ASP cc_start: 0.7478 (m-30) cc_final: 0.7259 (m-30) REVERT: A 392 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7345 (mm-30) REVERT: B 46 ARG cc_start: 0.6699 (mpp-170) cc_final: 0.6318 (mpp-170) REVERT: B 95 LEU cc_start: 0.7734 (mt) cc_final: 0.7475 (mt) REVERT: B 118 ASP cc_start: 0.7255 (p0) cc_final: 0.6900 (p0) REVERT: B 134 ARG cc_start: 0.7409 (ptt90) cc_final: 0.7151 (ptt90) REVERT: B 135 VAL cc_start: 0.8137 (t) cc_final: 0.7752 (m) REVERT: B 153 ASP cc_start: 0.7267 (t0) cc_final: 0.6935 (t0) REVERT: B 197 ARG cc_start: 0.7381 (mtp180) cc_final: 0.6825 (mtp180) REVERT: B 212 ASP cc_start: 0.7500 (t0) cc_final: 0.7099 (t0) REVERT: B 219 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7742 (mmt90) REVERT: B 300 LEU cc_start: 0.8084 (mt) cc_final: 0.7768 (mp) REVERT: B 333 ASP cc_start: 0.7553 (p0) cc_final: 0.7247 (p0) REVERT: P 11 ARG cc_start: 0.7573 (ttm170) cc_final: 0.7264 (ttm170) REVERT: R 268 LEU cc_start: 0.8127 (mt) cc_final: 0.7927 (mm) REVERT: R 279 ILE cc_start: 0.8158 (tp) cc_final: 0.7798 (tp) outliers start: 26 outliers final: 19 residues processed: 200 average time/residue: 0.1245 time to fit residues: 31.7295 Evaluate side-chains 206 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 85 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN R 124 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.142830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125746 restraints weight = 11452.056| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.27 r_work: 0.3478 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8309 Z= 0.130 Angle : 0.533 7.730 11255 Z= 0.287 Chirality : 0.042 0.183 1263 Planarity : 0.004 0.042 1433 Dihedral : 5.341 58.072 1118 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.31 % Allowed : 15.62 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1007 helix: 1.62 (0.26), residues: 383 sheet: 0.14 (0.33), residues: 225 loop : -0.86 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.016 0.001 TYR R 69 PHE 0.018 0.002 PHE R 306 TRP 0.015 0.002 TRP B 99 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8309) covalent geometry : angle 0.53298 (11255) hydrogen bonds : bond 0.03996 ( 425) hydrogen bonds : angle 4.60389 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8284 (tptp) cc_final: 0.7916 (tptp) REVERT: A 34 LYS cc_start: 0.8023 (ttpp) cc_final: 0.7795 (ttpp) REVERT: A 220 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6284 (t70) REVERT: A 222 PHE cc_start: 0.7477 (m-80) cc_final: 0.6240 (m-80) REVERT: A 342 ARG cc_start: 0.8337 (ttp-110) cc_final: 0.8086 (ttp-110) REVERT: A 346 LEU cc_start: 0.8236 (mp) cc_final: 0.8014 (mm) REVERT: A 350 THR cc_start: 0.8427 (m) cc_final: 0.8164 (p) REVERT: A 378 ASP cc_start: 0.7442 (m-30) cc_final: 0.7240 (m-30) REVERT: A 392 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 46 ARG cc_start: 0.6674 (mpp-170) cc_final: 0.6304 (mpp-170) REVERT: B 75 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: B 118 ASP cc_start: 0.7290 (p0) cc_final: 0.6914 (p0) REVERT: B 134 ARG cc_start: 0.7400 (ptt90) cc_final: 0.7153 (ptt90) REVERT: B 135 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7674 (m) REVERT: B 153 ASP cc_start: 0.7379 (t0) cc_final: 0.6972 (t0) REVERT: B 187 VAL cc_start: 0.8148 (m) cc_final: 0.7935 (t) REVERT: B 197 ARG cc_start: 0.7443 (mtp180) cc_final: 0.6845 (mtp180) REVERT: B 212 ASP cc_start: 0.7500 (t0) cc_final: 0.7127 (t0) REVERT: B 219 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7727 (mmt90) REVERT: B 230 ASN cc_start: 0.7784 (m-40) cc_final: 0.7465 (m-40) REVERT: B 253 PHE cc_start: 0.8649 (m-80) cc_final: 0.7982 (m-80) REVERT: B 298 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7081 (t70) REVERT: B 300 LEU cc_start: 0.8078 (mt) cc_final: 0.7617 (mp) REVERT: B 316 SER cc_start: 0.7814 (t) cc_final: 0.7488 (p) REVERT: B 333 ASP cc_start: 0.7574 (p0) cc_final: 0.7281 (p0) REVERT: R 150 MET cc_start: 0.7760 (tpp) cc_final: 0.7509 (mmt) REVERT: R 181 LEU cc_start: 0.8065 (tp) cc_final: 0.7826 (tp) REVERT: R 279 ILE cc_start: 0.8106 (tp) cc_final: 0.7737 (tp) outliers start: 29 outliers final: 22 residues processed: 205 average time/residue: 0.1185 time to fit residues: 30.8871 Evaluate side-chains 210 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 0.5980 chunk 96 optimal weight: 0.0170 chunk 79 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125178 restraints weight = 11332.968| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.11 r_work: 0.3481 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8309 Z= 0.149 Angle : 0.536 7.902 11255 Z= 0.288 Chirality : 0.043 0.194 1263 Planarity : 0.004 0.043 1433 Dihedral : 5.081 48.899 1118 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.10 % Allowed : 16.31 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1007 helix: 1.71 (0.26), residues: 383 sheet: -0.04 (0.32), residues: 229 loop : -0.85 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 283 TYR 0.017 0.001 TYR R 69 PHE 0.017 0.002 PHE R 306 TRP 0.016 0.002 TRP N 47 HIS 0.004 0.001 HIS R 124 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8309) covalent geometry : angle 0.53553 (11255) hydrogen bonds : bond 0.03986 ( 425) hydrogen bonds : angle 4.57590 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8296 (tptp) cc_final: 0.7924 (tptp) REVERT: A 34 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7827 (ttpp) REVERT: A 220 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6322 (t70) REVERT: A 222 PHE cc_start: 0.7496 (m-80) cc_final: 0.6310 (m-80) REVERT: A 230 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7923 (mp0) REVERT: A 232 ARG cc_start: 0.8415 (ptt-90) cc_final: 0.8197 (ptt-90) REVERT: A 346 LEU cc_start: 0.8315 (mp) cc_final: 0.8094 (mm) REVERT: A 350 THR cc_start: 0.8482 (m) cc_final: 0.8228 (p) REVERT: A 392 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7347 (mm-30) REVERT: B 46 ARG cc_start: 0.6728 (mpp-170) cc_final: 0.6388 (mpp-170) REVERT: B 118 ASP cc_start: 0.7266 (p0) cc_final: 0.6908 (p0) REVERT: B 134 ARG cc_start: 0.7387 (ptt90) cc_final: 0.7130 (ptt90) REVERT: B 135 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7660 (m) REVERT: B 153 ASP cc_start: 0.7497 (t0) cc_final: 0.7092 (t0) REVERT: B 197 ARG cc_start: 0.7348 (mtp180) cc_final: 0.6806 (mtp180) REVERT: B 212 ASP cc_start: 0.7545 (t0) cc_final: 0.7266 (t0) REVERT: B 219 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7733 (mmt90) REVERT: B 230 ASN cc_start: 0.7711 (m-40) cc_final: 0.7444 (m-40) REVERT: B 253 PHE cc_start: 0.8678 (m-80) cc_final: 0.8107 (m-80) REVERT: B 277 SER cc_start: 0.8191 (t) cc_final: 0.7729 (p) REVERT: B 298 ASP cc_start: 0.7467 (t70) cc_final: 0.7166 (t70) REVERT: B 300 LEU cc_start: 0.8082 (mt) cc_final: 0.7705 (mp) REVERT: B 316 SER cc_start: 0.7860 (t) cc_final: 0.7531 (p) REVERT: B 321 THR cc_start: 0.7957 (p) cc_final: 0.7753 (p) REVERT: B 333 ASP cc_start: 0.7516 (p0) cc_final: 0.7230 (p0) REVERT: R 181 LEU cc_start: 0.8110 (tp) cc_final: 0.7867 (tp) REVERT: R 279 ILE cc_start: 0.8075 (tp) cc_final: 0.7690 (tp) REVERT: R 300 LEU cc_start: 0.7797 (mm) cc_final: 0.7577 (mm) outliers start: 36 outliers final: 26 residues processed: 193 average time/residue: 0.1105 time to fit residues: 27.1934 Evaluate side-chains 200 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124260 restraints weight = 11239.515| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.10 r_work: 0.3474 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8309 Z= 0.185 Angle : 0.560 8.128 11255 Z= 0.299 Chirality : 0.043 0.178 1263 Planarity : 0.004 0.045 1433 Dihedral : 4.973 45.843 1118 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.65 % Allowed : 16.65 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 1007 helix: 1.65 (0.26), residues: 384 sheet: -0.13 (0.33), residues: 229 loop : -0.91 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 283 TYR 0.021 0.002 TYR R 69 PHE 0.016 0.002 PHE R 306 TRP 0.017 0.002 TRP N 47 HIS 0.004 0.001 HIS Y 44 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8309) covalent geometry : angle 0.55971 (11255) hydrogen bonds : bond 0.04109 ( 425) hydrogen bonds : angle 4.63584 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8280 (tptp) cc_final: 0.7890 (tptp) REVERT: A 220 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6303 (t70) REVERT: A 222 PHE cc_start: 0.7526 (m-80) cc_final: 0.6381 (m-80) REVERT: A 230 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7952 (mp0) REVERT: A 232 ARG cc_start: 0.8448 (ptt-90) cc_final: 0.8209 (ptt-90) REVERT: A 350 THR cc_start: 0.8488 (m) cc_final: 0.8251 (p) REVERT: A 392 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7347 (mm-30) REVERT: B 46 ARG cc_start: 0.6743 (mpp-170) cc_final: 0.6448 (mpp-170) REVERT: B 118 ASP cc_start: 0.7257 (p0) cc_final: 0.6920 (p0) REVERT: B 134 ARG cc_start: 0.7426 (ptt90) cc_final: 0.7146 (ptt90) REVERT: B 135 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7706 (m) REVERT: B 153 ASP cc_start: 0.7526 (t0) cc_final: 0.7157 (t0) REVERT: B 197 ARG cc_start: 0.7304 (mtp180) cc_final: 0.6788 (mtp180) REVERT: B 212 ASP cc_start: 0.7546 (t0) cc_final: 0.7254 (t0) REVERT: B 219 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7746 (mmt90) REVERT: B 246 ASP cc_start: 0.7643 (m-30) cc_final: 0.7393 (m-30) REVERT: B 253 PHE cc_start: 0.8696 (m-80) cc_final: 0.8240 (m-80) REVERT: B 277 SER cc_start: 0.8213 (t) cc_final: 0.7746 (p) REVERT: B 300 LEU cc_start: 0.8143 (mt) cc_final: 0.7793 (mp) REVERT: B 316 SER cc_start: 0.7863 (t) cc_final: 0.7524 (p) REVERT: B 321 THR cc_start: 0.7963 (p) cc_final: 0.7756 (p) REVERT: B 333 ASP cc_start: 0.7494 (p0) cc_final: 0.7221 (p0) REVERT: R 80 LEU cc_start: 0.8213 (tt) cc_final: 0.7991 (tt) REVERT: R 191 LEU cc_start: 0.7918 (tp) cc_final: 0.7687 (tp) REVERT: R 279 ILE cc_start: 0.8133 (tp) cc_final: 0.7751 (tp) REVERT: R 292 ILE cc_start: 0.8263 (pt) cc_final: 0.7934 (mm) outliers start: 32 outliers final: 29 residues processed: 198 average time/residue: 0.1213 time to fit residues: 30.5414 Evaluate side-chains 210 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 0.0370 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124966 restraints weight = 11359.119| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.12 r_work: 0.3478 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8309 Z= 0.153 Angle : 0.555 8.544 11255 Z= 0.296 Chirality : 0.043 0.211 1263 Planarity : 0.004 0.043 1433 Dihedral : 4.839 42.931 1118 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.33 % Allowed : 16.88 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.27), residues: 1007 helix: 1.79 (0.26), residues: 383 sheet: -0.10 (0.34), residues: 223 loop : -0.90 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 283 TYR 0.018 0.001 TYR R 69 PHE 0.015 0.002 PHE R 306 TRP 0.016 0.002 TRP N 47 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8309) covalent geometry : angle 0.55503 (11255) hydrogen bonds : bond 0.03931 ( 425) hydrogen bonds : angle 4.59648 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8276 (tptp) cc_final: 0.7899 (tptp) REVERT: A 220 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6319 (t70) REVERT: A 222 PHE cc_start: 0.7534 (m-80) cc_final: 0.6376 (m-80) REVERT: A 230 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7894 (mp0) REVERT: A 232 ARG cc_start: 0.8411 (ptt-90) cc_final: 0.8197 (ptt-90) REVERT: A 350 THR cc_start: 0.8485 (m) cc_final: 0.8245 (p) REVERT: A 392 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7320 (mm-30) REVERT: B 46 ARG cc_start: 0.6710 (mpp-170) cc_final: 0.6420 (mpp-170) REVERT: B 118 ASP cc_start: 0.7252 (p0) cc_final: 0.6915 (p0) REVERT: B 134 ARG cc_start: 0.7452 (ptt90) cc_final: 0.7180 (ptt90) REVERT: B 135 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7656 (m) REVERT: B 153 ASP cc_start: 0.7513 (t0) cc_final: 0.7144 (t0) REVERT: B 212 ASP cc_start: 0.7529 (t0) cc_final: 0.7177 (t0) REVERT: B 219 ARG cc_start: 0.8320 (tpp80) cc_final: 0.7746 (mmt90) REVERT: B 253 PHE cc_start: 0.8667 (m-80) cc_final: 0.8033 (m-80) REVERT: B 277 SER cc_start: 0.8203 (t) cc_final: 0.7738 (p) REVERT: B 300 LEU cc_start: 0.8078 (mt) cc_final: 0.7736 (mp) REVERT: B 316 SER cc_start: 0.7842 (t) cc_final: 0.7499 (p) REVERT: B 321 THR cc_start: 0.7940 (p) cc_final: 0.7729 (p) REVERT: B 333 ASP cc_start: 0.7520 (p0) cc_final: 0.7235 (p0) REVERT: R 80 LEU cc_start: 0.8282 (tt) cc_final: 0.8020 (tt) REVERT: R 81 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: R 150 MET cc_start: 0.7730 (tpp) cc_final: 0.7511 (mmt) REVERT: R 191 LEU cc_start: 0.7891 (tp) cc_final: 0.7655 (tp) REVERT: R 279 ILE cc_start: 0.8107 (tp) cc_final: 0.7732 (tp) REVERT: R 292 ILE cc_start: 0.8245 (pt) cc_final: 0.7916 (mm) outliers start: 38 outliers final: 30 residues processed: 196 average time/residue: 0.1142 time to fit residues: 28.8101 Evaluate side-chains 210 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 81 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125126 restraints weight = 11280.184| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.12 r_work: 0.3482 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8309 Z= 0.147 Angle : 0.553 7.709 11255 Z= 0.293 Chirality : 0.043 0.222 1263 Planarity : 0.004 0.050 1433 Dihedral : 4.770 41.290 1118 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.22 % Allowed : 17.33 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.27), residues: 1007 helix: 1.84 (0.26), residues: 388 sheet: -0.03 (0.33), residues: 222 loop : -0.83 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 283 TYR 0.018 0.001 TYR R 69 PHE 0.015 0.001 PHE R 306 TRP 0.015 0.002 TRP N 47 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8309) covalent geometry : angle 0.55285 (11255) hydrogen bonds : bond 0.03855 ( 425) hydrogen bonds : angle 4.54465 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8293 (tptp) cc_final: 0.7915 (tptp) REVERT: A 220 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6288 (t70) REVERT: A 222 PHE cc_start: 0.7503 (m-80) cc_final: 0.6319 (m-80) REVERT: A 350 THR cc_start: 0.8449 (m) cc_final: 0.8210 (p) REVERT: A 392 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 46 ARG cc_start: 0.6723 (mpp-170) cc_final: 0.6419 (mpp-170) REVERT: B 67 SER cc_start: 0.8256 (m) cc_final: 0.7986 (p) REVERT: B 118 ASP cc_start: 0.7249 (p0) cc_final: 0.6909 (p0) REVERT: B 134 ARG cc_start: 0.7434 (ptt90) cc_final: 0.7144 (ptt90) REVERT: B 135 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7631 (m) REVERT: B 153 ASP cc_start: 0.7520 (t0) cc_final: 0.7141 (t0) REVERT: B 188 MET cc_start: 0.7734 (mmm) cc_final: 0.7498 (mtm) REVERT: B 212 ASP cc_start: 0.7544 (t0) cc_final: 0.7242 (t0) REVERT: B 219 ARG cc_start: 0.8319 (tpp80) cc_final: 0.7735 (mmt90) REVERT: B 253 PHE cc_start: 0.8591 (m-80) cc_final: 0.8029 (m-80) REVERT: B 277 SER cc_start: 0.8202 (t) cc_final: 0.7724 (p) REVERT: B 298 ASP cc_start: 0.7477 (t70) cc_final: 0.7225 (t70) REVERT: B 300 LEU cc_start: 0.8104 (mt) cc_final: 0.7752 (mp) REVERT: B 316 SER cc_start: 0.7792 (t) cc_final: 0.7437 (p) REVERT: B 333 ASP cc_start: 0.7610 (p0) cc_final: 0.7302 (p0) REVERT: N 34 MET cc_start: 0.8181 (mmm) cc_final: 0.7914 (tpt) REVERT: R 80 LEU cc_start: 0.8269 (tt) cc_final: 0.7999 (tt) REVERT: R 81 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: R 150 MET cc_start: 0.7741 (tpp) cc_final: 0.7506 (mmt) REVERT: R 181 LEU cc_start: 0.8136 (tp) cc_final: 0.7895 (tp) REVERT: R 279 ILE cc_start: 0.8108 (tp) cc_final: 0.7734 (tp) outliers start: 37 outliers final: 31 residues processed: 195 average time/residue: 0.1134 time to fit residues: 28.6271 Evaluate side-chains 209 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 81 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124224 restraints weight = 11315.863| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.09 r_work: 0.3469 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8309 Z= 0.174 Angle : 0.573 9.159 11255 Z= 0.301 Chirality : 0.044 0.223 1263 Planarity : 0.004 0.056 1433 Dihedral : 4.810 40.892 1118 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.65 % Allowed : 18.13 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.27), residues: 1007 helix: 1.89 (0.26), residues: 383 sheet: -0.06 (0.33), residues: 222 loop : -0.80 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 283 TYR 0.020 0.002 TYR R 69 PHE 0.015 0.002 PHE R 306 TRP 0.018 0.002 TRP B 99 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8309) covalent geometry : angle 0.57341 (11255) hydrogen bonds : bond 0.04009 ( 425) hydrogen bonds : angle 4.59413 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8287 (tptp) cc_final: 0.7909 (tptp) REVERT: A 220 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6257 (t70) REVERT: A 222 PHE cc_start: 0.7517 (m-80) cc_final: 0.6315 (m-80) REVERT: A 228 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.7650 (ptm160) REVERT: A 350 THR cc_start: 0.8465 (m) cc_final: 0.8229 (p) REVERT: A 392 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 46 ARG cc_start: 0.6732 (mpp-170) cc_final: 0.6437 (mpp-170) REVERT: B 48 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7240 (mmt-90) REVERT: B 67 SER cc_start: 0.8259 (m) cc_final: 0.7982 (p) REVERT: B 98 SER cc_start: 0.7969 (m) cc_final: 0.7684 (p) REVERT: B 118 ASP cc_start: 0.7251 (p0) cc_final: 0.6910 (p0) REVERT: B 134 ARG cc_start: 0.7520 (ptt90) cc_final: 0.7199 (ptt90) REVERT: B 135 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7675 (m) REVERT: B 143 THR cc_start: 0.8534 (t) cc_final: 0.8234 (p) REVERT: B 153 ASP cc_start: 0.7577 (t0) cc_final: 0.7221 (t0) REVERT: B 188 MET cc_start: 0.7723 (mmm) cc_final: 0.7496 (mtm) REVERT: B 212 ASP cc_start: 0.7548 (t0) cc_final: 0.7255 (t0) REVERT: B 219 ARG cc_start: 0.8332 (tpp80) cc_final: 0.7753 (mmt90) REVERT: B 253 PHE cc_start: 0.8575 (m-80) cc_final: 0.7969 (m-80) REVERT: B 277 SER cc_start: 0.8196 (t) cc_final: 0.7687 (p) REVERT: B 298 ASP cc_start: 0.7535 (t70) cc_final: 0.7205 (t70) REVERT: B 316 SER cc_start: 0.7871 (t) cc_final: 0.7513 (p) REVERT: B 333 ASP cc_start: 0.7665 (p0) cc_final: 0.7357 (p0) REVERT: R 81 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: R 181 LEU cc_start: 0.8146 (tp) cc_final: 0.7904 (tp) REVERT: R 192 PHE cc_start: 0.7420 (m-10) cc_final: 0.6970 (m-80) REVERT: R 279 ILE cc_start: 0.8144 (tp) cc_final: 0.7773 (tp) outliers start: 32 outliers final: 27 residues processed: 199 average time/residue: 0.1052 time to fit residues: 27.5116 Evaluate side-chains 209 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 81 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** 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 = 0.3793 r_free = 0.3793 target = 0.140788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124420 restraints weight = 11295.554| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.10 r_work: 0.3470 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8309 Z= 0.171 Angle : 0.583 9.643 11255 Z= 0.303 Chirality : 0.044 0.231 1263 Planarity : 0.004 0.058 1433 Dihedral : 4.822 39.541 1118 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.65 % Allowed : 18.70 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1007 helix: 1.77 (0.26), residues: 384 sheet: -0.06 (0.33), residues: 231 loop : -0.86 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 283 TYR 0.020 0.002 TYR R 69 PHE 0.019 0.002 PHE R 306 TRP 0.017 0.002 TRP N 47 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8309) covalent geometry : angle 0.58261 (11255) hydrogen bonds : bond 0.03989 ( 425) hydrogen bonds : angle 4.60406 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8281 (tptp) cc_final: 0.7907 (tptp) REVERT: A 220 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6267 (t70) REVERT: A 222 PHE cc_start: 0.7510 (m-80) cc_final: 0.6326 (m-80) REVERT: A 228 ARG cc_start: 0.8349 (mtp-110) cc_final: 0.7660 (ptm160) REVERT: A 350 THR cc_start: 0.8464 (m) cc_final: 0.8225 (p) REVERT: A 392 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7312 (mm-30) REVERT: B 46 ARG cc_start: 0.6743 (mpp-170) cc_final: 0.6457 (mpp-170) REVERT: B 57 LYS cc_start: 0.8576 (pttm) cc_final: 0.8265 (pttm) REVERT: B 67 SER cc_start: 0.8256 (m) cc_final: 0.7987 (p) REVERT: B 75 GLN cc_start: 0.8038 (mt0) cc_final: 0.7665 (mt0) REVERT: B 98 SER cc_start: 0.7973 (m) cc_final: 0.7721 (p) REVERT: B 118 ASP cc_start: 0.7254 (p0) cc_final: 0.6917 (p0) REVERT: B 134 ARG cc_start: 0.7506 (ptt90) cc_final: 0.7177 (ptt90) REVERT: B 135 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7681 (m) REVERT: B 153 ASP cc_start: 0.7572 (t0) cc_final: 0.7214 (t0) REVERT: B 212 ASP cc_start: 0.7554 (t0) cc_final: 0.7256 (t0) REVERT: B 219 ARG cc_start: 0.8329 (tpp80) cc_final: 0.7748 (mmt90) REVERT: B 253 PHE cc_start: 0.8568 (m-80) cc_final: 0.7964 (m-80) REVERT: B 277 SER cc_start: 0.8187 (t) cc_final: 0.7692 (p) REVERT: B 298 ASP cc_start: 0.7569 (t70) cc_final: 0.7223 (t70) REVERT: B 316 SER cc_start: 0.7796 (t) cc_final: 0.7451 (p) REVERT: B 333 ASP cc_start: 0.7677 (p0) cc_final: 0.7369 (p0) REVERT: N 34 MET cc_start: 0.8168 (mmm) cc_final: 0.7872 (tpt) REVERT: R 181 LEU cc_start: 0.8149 (tp) cc_final: 0.7911 (tp) REVERT: R 192 PHE cc_start: 0.7413 (m-10) cc_final: 0.6983 (m-80) REVERT: R 279 ILE cc_start: 0.8144 (tp) cc_final: 0.7772 (tp) outliers start: 32 outliers final: 29 residues processed: 192 average time/residue: 0.1115 time to fit residues: 27.8293 Evaluate side-chains 205 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** 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 = 0.3794 r_free = 0.3794 target = 0.140705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124240 restraints weight = 11321.389| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.10 r_work: 0.3472 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8309 Z= 0.177 Angle : 0.593 10.249 11255 Z= 0.306 Chirality : 0.044 0.221 1263 Planarity : 0.004 0.060 1433 Dihedral : 4.832 38.494 1118 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.88 % Allowed : 18.47 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1007 helix: 1.76 (0.26), residues: 384 sheet: 0.01 (0.33), residues: 229 loop : -0.89 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 283 TYR 0.021 0.002 TYR R 69 PHE 0.020 0.002 PHE R 306 TRP 0.017 0.002 TRP N 47 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8309) covalent geometry : angle 0.59282 (11255) hydrogen bonds : bond 0.04016 ( 425) hydrogen bonds : angle 4.61608 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.78 seconds wall clock time: 36 minutes 1.91 seconds (2161.91 seconds total)