Starting phenix.real_space_refine on Wed Mar 12 16:20:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v9m_31825/03_2025/7v9m_31825.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9m_31825/03_2025/7v9m_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_2025/7v9m_31825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9m_31825/03_2025/7v9m_31825.map" model { file = "/net/cci-nas-00/data/ceres_data/7v9m_31825/03_2025/7v9m_31825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9m_31825/03_2025/7v9m_31825.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.96, per 1000 atoms: 0.61 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 2.34 Time building geometry restraints manager: 2.29 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: 0.740 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.520 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- 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= 0.272 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 : 4.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.003 TRP A 234 HIS 0.005 0.001 HIS R 124 PHE 0.025 0.002 PHE R 306 TYR 0.028 0.003 TYR R 69 ARG 0.046 0.006 ARG N 67 *********************** 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 : 1.003 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: 0.7224 (pttm) REVERT: B 61 MET cc_start: 0.6441 (ppp) cc_final: 0.6132 (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: 0.6539 (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: 0.7622 (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: 0.8013 (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: 0.3034 time to fit residues: 87.9769 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 : 1.097 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126138 restraints weight = 11314.516| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.08 r_work: 0.3485 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8309 Z= 0.206 Angle : 0.603 8.267 11255 Z= 0.329 Chirality : 0.044 0.170 1263 Planarity : 0.004 0.037 1433 Dihedral : 6.119 70.571 1118 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.82 % Allowed : 11.40 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1007 helix: 1.14 (0.26), residues: 381 sheet: 0.38 (0.34), residues: 225 loop : -0.78 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.005 0.001 HIS B 54 PHE 0.022 0.002 PHE R 306 TYR 0.016 0.001 TYR R 69 ARG 0.004 0.000 ARG P 11 *********************** 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: 16 poor density : 194 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8253 (tptp) cc_final: 0.7943 (tptp) REVERT: A 220 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6505 (t70) REVERT: A 222 PHE cc_start: 0.7537 (m-80) cc_final: 0.6455 (m-80) REVERT: A 230 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 346 LEU cc_start: 0.8457 (mp) cc_final: 0.8201 (mm) REVERT: A 347 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7721 (ttp80) REVERT: A 350 THR cc_start: 0.8596 (m) cc_final: 0.8311 (p) REVERT: A 392 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 46 ARG cc_start: 0.6560 (mpp-170) cc_final: 0.6322 (mpp-170) REVERT: B 95 LEU cc_start: 0.7756 (mt) cc_final: 0.7502 (mt) REVERT: B 101 MET cc_start: 0.8001 (mtp) cc_final: 0.7795 (mtp) REVERT: B 118 ASP cc_start: 0.7173 (p0) cc_final: 0.6781 (p0) REVERT: B 134 ARG cc_start: 0.7429 (ptt90) cc_final: 0.7211 (ptt90) REVERT: B 135 VAL cc_start: 0.8151 (t) cc_final: 0.7776 (m) REVERT: B 165 THR cc_start: 0.8210 (p) cc_final: 0.7880 (t) REVERT: B 197 ARG cc_start: 0.7488 (mtp180) cc_final: 0.6885 (mtp180) REVERT: B 219 ARG cc_start: 0.8288 (tpp80) cc_final: 0.7873 (mmt90) REVERT: B 263 THR cc_start: 0.8046 (m) cc_final: 0.7805 (p) REVERT: B 300 LEU cc_start: 0.8130 (mt) cc_final: 0.7814 (mp) REVERT: B 318 LEU cc_start: 0.7894 (tt) cc_final: 0.7654 (tp) REVERT: B 333 ASP cc_start: 0.7510 (p0) cc_final: 0.7236 (p0) REVERT: P 11 ARG cc_start: 0.7552 (ttm170) cc_final: 0.7087 (ttm170) REVERT: R 109 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8355 (mt) REVERT: R 231 VAL cc_start: 0.7876 (m) cc_final: 0.7667 (p) REVERT: R 279 ILE cc_start: 0.8163 (tp) cc_final: 0.7812 (tp) REVERT: Y 21 MET cc_start: 0.7833 (tpp) cc_final: 0.7631 (tpp) outliers start: 16 outliers final: 9 residues processed: 202 average time/residue: 0.2629 time to fit residues: 67.5597 Evaluate side-chains 202 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 262 MET Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU 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 83 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 82 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.142904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125949 restraints weight = 11338.465| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.24 r_work: 0.3481 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8309 Z= 0.186 Angle : 0.549 7.540 11255 Z= 0.298 Chirality : 0.043 0.174 1263 Planarity : 0.004 0.043 1433 Dihedral : 5.580 63.876 1118 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.17 % Allowed : 15.62 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1007 helix: 1.49 (0.26), residues: 383 sheet: 0.22 (0.34), residues: 225 loop : -0.82 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.003 0.001 HIS B 54 PHE 0.020 0.002 PHE R 306 TYR 0.013 0.001 TYR N 60 ARG 0.008 0.000 ARG A 283 *********************** 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 208 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8304 (tptp) cc_final: 0.7950 (tptp) REVERT: A 220 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6269 (t70) REVERT: A 222 PHE cc_start: 0.7464 (m-80) cc_final: 0.6219 (m-80) REVERT: A 230 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7869 (mt-10) REVERT: A 342 ARG cc_start: 0.8343 (ttp-110) cc_final: 0.8090 (ttp-110) REVERT: A 346 LEU cc_start: 0.8218 (mp) cc_final: 0.7988 (mm) REVERT: A 350 THR cc_start: 0.8425 (m) cc_final: 0.8155 (p) REVERT: A 392 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 46 ARG cc_start: 0.6652 (mpp-170) cc_final: 0.6284 (mpp-170) REVERT: B 118 ASP cc_start: 0.7270 (p0) cc_final: 0.6909 (p0) REVERT: B 134 ARG cc_start: 0.7437 (ptt90) cc_final: 0.7180 (ptt90) REVERT: B 135 VAL cc_start: 0.8099 (t) cc_final: 0.7704 (m) REVERT: B 153 ASP cc_start: 0.7228 (t0) cc_final: 0.6882 (t0) REVERT: B 180 PHE cc_start: 0.8099 (m-80) cc_final: 0.7887 (m-10) REVERT: B 187 VAL cc_start: 0.8236 (m) cc_final: 0.7908 (t) REVERT: B 197 ARG cc_start: 0.7335 (mtp180) cc_final: 0.6746 (mtp180) REVERT: B 212 ASP cc_start: 0.7453 (t0) cc_final: 0.7113 (t0) REVERT: B 283 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7517 (tpt170) REVERT: B 298 ASP cc_start: 0.7601 (t0) cc_final: 0.7346 (t70) REVERT: B 300 LEU cc_start: 0.8021 (mt) cc_final: 0.7591 (mp) REVERT: B 318 LEU cc_start: 0.7999 (tt) cc_final: 0.7782 (tp) REVERT: B 333 ASP cc_start: 0.7568 (p0) cc_final: 0.7275 (p0) REVERT: P 11 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7169 (ttm170) REVERT: R 279 ILE cc_start: 0.8143 (tp) cc_final: 0.7816 (tp) REVERT: Y 21 MET cc_start: 0.7692 (tpp) cc_final: 0.7422 (tpp) outliers start: 19 outliers final: 12 residues processed: 198 average time/residue: 0.2845 time to fit residues: 71.5233 Evaluate side-chains 203 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 181 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.0370 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 0.0040 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4470 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.142881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125857 restraints weight = 11211.477| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.23 r_work: 0.3478 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2338 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= 0.184 Angle : 0.530 7.524 11255 Z= 0.286 Chirality : 0.042 0.179 1263 Planarity : 0.004 0.041 1433 Dihedral : 5.348 58.007 1118 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.42 % Allowed : 16.31 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1007 helix: 1.69 (0.26), residues: 383 sheet: 0.23 (0.33), residues: 223 loop : -0.80 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.018 0.002 PHE R 306 TYR 0.015 0.001 TYR N 32 ARG 0.008 0.000 ARG A 283 *********************** 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 211 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8264 (tptp) cc_final: 0.7893 (tptp) REVERT: A 220 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6299 (t70) REVERT: A 222 PHE cc_start: 0.7450 (m-80) cc_final: 0.6253 (m-80) REVERT: A 230 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 233 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8218 (mmmt) REVERT: A 342 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.8114 (ttp-110) REVERT: A 350 THR cc_start: 0.8428 (m) cc_final: 0.8172 (p) REVERT: A 392 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7358 (mm-30) REVERT: B 46 ARG cc_start: 0.6668 (mpp-170) cc_final: 0.6312 (mpp-170) REVERT: B 57 LYS cc_start: 0.8570 (pttp) cc_final: 0.8221 (pttp) REVERT: B 118 ASP cc_start: 0.7279 (p0) cc_final: 0.6921 (p0) REVERT: B 134 ARG cc_start: 0.7435 (ptt90) cc_final: 0.7168 (ptt90) REVERT: B 135 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7643 (m) REVERT: B 153 ASP cc_start: 0.7327 (t0) cc_final: 0.6943 (t0) REVERT: B 197 ARG cc_start: 0.7442 (mtp180) cc_final: 0.6851 (mtp180) REVERT: B 212 ASP cc_start: 0.7475 (t0) cc_final: 0.7117 (t0) REVERT: B 219 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7718 (mmt90) REVERT: B 246 ASP cc_start: 0.7764 (m-30) cc_final: 0.7485 (m-30) REVERT: B 283 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7470 (tpt170) REVERT: B 300 LEU cc_start: 0.8042 (mt) cc_final: 0.7701 (mp) REVERT: B 316 SER cc_start: 0.7830 (t) cc_final: 0.7494 (p) REVERT: B 318 LEU cc_start: 0.8006 (tt) cc_final: 0.7788 (tp) REVERT: B 333 ASP cc_start: 0.7563 (p0) cc_final: 0.7289 (p0) REVERT: R 279 ILE cc_start: 0.8062 (tp) cc_final: 0.7741 (tp) REVERT: Y 21 MET cc_start: 0.7744 (tpp) cc_final: 0.7452 (tpp) outliers start: 30 outliers final: 24 residues processed: 194 average time/residue: 0.2814 time to fit residues: 69.0712 Evaluate side-chains 206 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP 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 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 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 N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU 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 290 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 5 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.141273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124097 restraints weight = 11116.329| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.23 r_work: 0.3465 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8309 Z= 0.256 Angle : 0.549 7.558 11255 Z= 0.297 Chirality : 0.044 0.214 1263 Planarity : 0.004 0.047 1433 Dihedral : 5.283 54.807 1118 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.76 % Allowed : 16.88 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1007 helix: 1.79 (0.26), residues: 376 sheet: 0.07 (0.34), residues: 221 loop : -0.93 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 47 HIS 0.010 0.001 HIS R 124 PHE 0.018 0.002 PHE R 306 TYR 0.015 0.002 TYR N 32 ARG 0.009 0.000 ARG A 283 *********************** 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 217 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8243 (tptp) cc_final: 0.7860 (tptp) REVERT: A 220 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6262 (t70) REVERT: A 222 PHE cc_start: 0.7438 (m-80) cc_final: 0.6196 (m-80) REVERT: A 230 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7959 (mt-10) REVERT: A 342 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.8081 (ttp-110) REVERT: A 346 LEU cc_start: 0.8244 (mp) cc_final: 0.7997 (mm) REVERT: A 350 THR cc_start: 0.8420 (m) cc_final: 0.8160 (p) REVERT: A 392 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7348 (mm-30) REVERT: B 46 ARG cc_start: 0.6701 (mpp-170) cc_final: 0.6326 (mpp-170) REVERT: B 75 GLN cc_start: 0.8098 (mt0) cc_final: 0.7866 (mt0) REVERT: B 118 ASP cc_start: 0.7298 (p0) cc_final: 0.6944 (p0) REVERT: B 134 ARG cc_start: 0.7432 (ptt90) cc_final: 0.7154 (ptt90) REVERT: B 135 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7674 (m) REVERT: B 153 ASP cc_start: 0.7452 (t0) cc_final: 0.7013 (t0) REVERT: B 197 ARG cc_start: 0.7356 (mtp180) cc_final: 0.6753 (mtp180) REVERT: B 212 ASP cc_start: 0.7541 (t0) cc_final: 0.7206 (t0) REVERT: B 219 ARG cc_start: 0.8264 (tpp80) cc_final: 0.7762 (mmt90) REVERT: B 253 PHE cc_start: 0.8650 (m-80) cc_final: 0.7993 (m-80) REVERT: B 298 ASP cc_start: 0.7611 (t70) cc_final: 0.7179 (t0) REVERT: B 300 LEU cc_start: 0.8121 (mt) cc_final: 0.7632 (mp) REVERT: B 316 SER cc_start: 0.7937 (t) cc_final: 0.7574 (p) REVERT: B 321 THR cc_start: 0.7936 (p) cc_final: 0.7731 (p) REVERT: B 333 ASP cc_start: 0.7554 (p0) cc_final: 0.7273 (p0) REVERT: R 150 MET cc_start: 0.7882 (tpp) cc_final: 0.7577 (mmt) REVERT: R 191 LEU cc_start: 0.7768 (tp) cc_final: 0.7537 (tp) REVERT: R 279 ILE cc_start: 0.8083 (tp) cc_final: 0.7748 (tp) REVERT: Y 21 MET cc_start: 0.7746 (tpp) cc_final: 0.7455 (tpp) outliers start: 33 outliers final: 25 residues processed: 202 average time/residue: 0.2618 time to fit residues: 67.5689 Evaluate side-chains 209 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP 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 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 228 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.142440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125807 restraints weight = 11262.309| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.11 r_work: 0.3489 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8309 Z= 0.194 Angle : 0.541 7.561 11255 Z= 0.289 Chirality : 0.042 0.187 1263 Planarity : 0.004 0.048 1433 Dihedral : 4.942 46.431 1118 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.56 % Allowed : 16.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1007 helix: 1.89 (0.26), residues: 378 sheet: 0.05 (0.34), residues: 221 loop : -0.88 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 47 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE R 306 TYR 0.009 0.001 TYR B 105 ARG 0.010 0.000 ARG A 283 *********************** 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 221 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8286 (tptp) cc_final: 0.7902 (tptp) REVERT: A 220 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6304 (t70) REVERT: A 222 PHE cc_start: 0.7483 (m-80) cc_final: 0.6314 (m-80) REVERT: A 233 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8232 (mmmt) REVERT: A 350 THR cc_start: 0.8462 (m) cc_final: 0.8216 (p) REVERT: A 392 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7324 (mm-30) REVERT: B 46 ARG cc_start: 0.6676 (mpp-170) cc_final: 0.6349 (mpp-170) REVERT: B 67 SER cc_start: 0.8255 (m) cc_final: 0.7996 (p) REVERT: B 118 ASP cc_start: 0.7245 (p0) cc_final: 0.6881 (p0) REVERT: B 134 ARG cc_start: 0.7379 (ptt90) cc_final: 0.7117 (ptt90) REVERT: B 135 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7656 (m) REVERT: B 153 ASP cc_start: 0.7500 (t0) cc_final: 0.7138 (t0) REVERT: B 197 ARG cc_start: 0.7289 (mtp180) cc_final: 0.6721 (mtp180) REVERT: B 212 ASP cc_start: 0.7535 (t0) cc_final: 0.7255 (t0) REVERT: B 219 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7791 (mmt90) REVERT: B 246 ASP cc_start: 0.7658 (m-30) cc_final: 0.7408 (m-30) REVERT: B 253 PHE cc_start: 0.8662 (m-80) cc_final: 0.8114 (m-80) REVERT: B 283 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7544 (ttt90) REVERT: B 298 ASP cc_start: 0.7503 (t70) cc_final: 0.7251 (t0) REVERT: B 300 LEU cc_start: 0.8173 (mt) cc_final: 0.7687 (mp) REVERT: B 316 SER cc_start: 0.7818 (t) cc_final: 0.7470 (p) REVERT: B 333 ASP cc_start: 0.7528 (p0) cc_final: 0.7247 (p0) REVERT: N 34 MET cc_start: 0.8160 (mmm) cc_final: 0.7938 (tpt) REVERT: P 11 ARG cc_start: 0.7678 (ttm170) cc_final: 0.7428 (tpp80) REVERT: R 181 LEU cc_start: 0.8126 (tp) cc_final: 0.7883 (tp) REVERT: R 279 ILE cc_start: 0.8060 (tp) cc_final: 0.7776 (tp) REVERT: Y 21 MET cc_start: 0.7799 (tpp) cc_final: 0.7508 (tpp) outliers start: 40 outliers final: 31 residues processed: 202 average time/residue: 0.2724 time to fit residues: 69.6624 Evaluate side-chains 211 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 228 ASP Chi-restraints excluded: chain B residue 263 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 N residue 105 ARG 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 198 SER Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.141085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124492 restraints weight = 11295.653| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.10 r_work: 0.3468 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2761 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= 0.248 Angle : 0.565 7.680 11255 Z= 0.301 Chirality : 0.043 0.200 1263 Planarity : 0.004 0.044 1433 Dihedral : 4.909 43.724 1118 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.10 % Allowed : 17.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 1007 helix: 1.90 (0.26), residues: 378 sheet: -0.14 (0.34), residues: 219 loop : -0.90 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.004 0.001 HIS Y 44 PHE 0.016 0.002 PHE R 306 TYR 0.011 0.002 TYR B 145 ARG 0.012 0.000 ARG A 283 *********************** 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 216 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8260 (tptp) cc_final: 0.7888 (tptp) REVERT: A 220 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6317 (t70) REVERT: A 222 PHE cc_start: 0.7538 (m-80) cc_final: 0.6417 (m-80) REVERT: A 350 THR cc_start: 0.8492 (m) cc_final: 0.8250 (p) REVERT: A 392 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7353 (mm-30) REVERT: B 46 ARG cc_start: 0.6741 (mpp-170) cc_final: 0.6454 (mpp-170) REVERT: B 118 ASP cc_start: 0.7257 (p0) cc_final: 0.6905 (p0) REVERT: B 134 ARG cc_start: 0.7382 (ptt90) cc_final: 0.7145 (ptt90) REVERT: B 135 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7683 (m) REVERT: B 153 ASP cc_start: 0.7527 (t0) cc_final: 0.7160 (t0) REVERT: B 197 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6784 (mtp180) REVERT: B 212 ASP cc_start: 0.7555 (t0) cc_final: 0.7190 (t0) REVERT: B 219 ARG cc_start: 0.8351 (tpp80) cc_final: 0.7822 (mmt90) REVERT: B 253 PHE cc_start: 0.8644 (m-80) cc_final: 0.8066 (m-80) REVERT: B 277 SER cc_start: 0.8188 (t) cc_final: 0.7731 (p) REVERT: B 283 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7627 (ttt90) REVERT: B 300 LEU cc_start: 0.8188 (mt) cc_final: 0.7835 (mp) REVERT: B 316 SER cc_start: 0.7821 (t) cc_final: 0.7436 (p) REVERT: B 333 ASP cc_start: 0.7539 (p0) cc_final: 0.7244 (p0) REVERT: R 279 ILE cc_start: 0.8107 (tp) cc_final: 0.7840 (tp) REVERT: Y 21 MET cc_start: 0.7808 (tpp) cc_final: 0.7524 (tpp) outliers start: 36 outliers final: 31 residues processed: 199 average time/residue: 0.2539 time to fit residues: 65.2469 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 : 0.907 ------------------------------------------------------------------------------- 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 63 SER Chi-restraints excluded: chain N residue 105 ARG 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 154 SER 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 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 7 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.143325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126814 restraints weight = 11327.307| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.11 r_work: 0.3501 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8309 Z= 0.156 Angle : 0.537 8.101 11255 Z= 0.283 Chirality : 0.042 0.189 1263 Planarity : 0.004 0.047 1433 Dihedral : 4.670 40.190 1118 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.42 % Allowed : 18.59 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1007 helix: 2.01 (0.26), residues: 383 sheet: 0.03 (0.34), residues: 219 loop : -0.80 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS B 266 PHE 0.014 0.001 PHE R 306 TYR 0.008 0.001 TYR B 105 ARG 0.012 0.000 ARG A 283 *********************** 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 209 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8288 (tptp) cc_final: 0.7920 (tptp) REVERT: A 34 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7906 (ttpp) REVERT: A 220 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6343 (t70) REVERT: A 222 PHE cc_start: 0.7509 (m-80) cc_final: 0.6433 (m-80) REVERT: A 228 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7598 (ptm160) REVERT: A 350 THR cc_start: 0.8478 (m) cc_final: 0.8238 (p) REVERT: A 392 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7313 (mm-30) REVERT: B 46 ARG cc_start: 0.6643 (mpp-170) cc_final: 0.6341 (mpp-170) REVERT: B 118 ASP cc_start: 0.7263 (p0) cc_final: 0.6916 (p0) REVERT: B 134 ARG cc_start: 0.7434 (ptt90) cc_final: 0.7160 (ptt90) REVERT: B 135 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7572 (m) REVERT: B 153 ASP cc_start: 0.7571 (t0) cc_final: 0.7201 (t0) REVERT: B 212 ASP cc_start: 0.7520 (t0) cc_final: 0.7288 (t0) REVERT: B 219 ARG cc_start: 0.8343 (tpp80) cc_final: 0.7807 (mmt90) REVERT: B 253 PHE cc_start: 0.8547 (m-80) cc_final: 0.8051 (m-80) REVERT: B 277 SER cc_start: 0.8162 (t) cc_final: 0.7690 (p) REVERT: B 283 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7574 (ttt90) REVERT: B 298 ASP cc_start: 0.7373 (t70) cc_final: 0.7067 (t0) REVERT: B 300 LEU cc_start: 0.8149 (mt) cc_final: 0.7665 (mp) REVERT: B 316 SER cc_start: 0.7677 (t) cc_final: 0.7319 (p) REVERT: B 333 ASP cc_start: 0.7580 (p0) cc_final: 0.7290 (p0) REVERT: N 34 MET cc_start: 0.8126 (mmm) cc_final: 0.7897 (tpt) REVERT: R 181 LEU cc_start: 0.8140 (tp) cc_final: 0.7911 (tp) REVERT: R 279 ILE cc_start: 0.8007 (tp) cc_final: 0.7733 (tp) REVERT: Y 21 MET cc_start: 0.7815 (tpp) cc_final: 0.7532 (tpp) outliers start: 30 outliers final: 27 residues processed: 193 average time/residue: 0.2564 time to fit residues: 63.3357 Evaluate side-chains 204 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG 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 154 SER 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 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 32 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 71 optimal weight: 0.0040 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.142156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125561 restraints weight = 11456.064| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.12 r_work: 0.3479 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3011 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= 0.199 Angle : 0.555 8.383 11255 Z= 0.291 Chirality : 0.043 0.226 1263 Planarity : 0.004 0.053 1433 Dihedral : 4.678 39.306 1118 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.76 % Allowed : 18.81 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 1007 helix: 1.90 (0.26), residues: 390 sheet: -0.07 (0.33), residues: 224 loop : -0.78 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS B 266 PHE 0.015 0.001 PHE R 306 TYR 0.011 0.001 TYR N 32 ARG 0.013 0.000 ARG A 283 *********************** 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 215 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8313 (tptp) cc_final: 0.7950 (tptp) REVERT: A 220 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6311 (t70) REVERT: A 222 PHE cc_start: 0.7539 (m-80) cc_final: 0.6381 (m-80) REVERT: A 228 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.7654 (ptm160) REVERT: A 350 THR cc_start: 0.8479 (m) cc_final: 0.8235 (p) REVERT: A 392 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7337 (mm-30) REVERT: B 46 ARG cc_start: 0.6661 (mpp-170) cc_final: 0.6390 (mpp-170) REVERT: B 67 SER cc_start: 0.8295 (m) cc_final: 0.7983 (p) REVERT: B 98 SER cc_start: 0.7995 (m) cc_final: 0.7705 (p) REVERT: B 118 ASP cc_start: 0.7280 (p0) cc_final: 0.6945 (p0) REVERT: B 134 ARG cc_start: 0.7505 (ptt90) cc_final: 0.7189 (ptt90) REVERT: B 135 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7625 (m) REVERT: B 153 ASP cc_start: 0.7582 (t0) cc_final: 0.7212 (t0) REVERT: B 212 ASP cc_start: 0.7549 (t0) cc_final: 0.7282 (t0) REVERT: B 219 ARG cc_start: 0.8332 (tpp80) cc_final: 0.7732 (mmt90) REVERT: B 253 PHE cc_start: 0.8570 (m-80) cc_final: 0.8064 (m-80) REVERT: B 277 SER cc_start: 0.8163 (t) cc_final: 0.7691 (p) REVERT: B 283 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7507 (ttt90) REVERT: B 298 ASP cc_start: 0.7420 (t70) cc_final: 0.7094 (t0) REVERT: B 300 LEU cc_start: 0.8154 (mt) cc_final: 0.7666 (mp) REVERT: B 316 SER cc_start: 0.7767 (t) cc_final: 0.7406 (p) REVERT: B 333 ASP cc_start: 0.7589 (p0) cc_final: 0.7282 (p0) REVERT: R 279 ILE cc_start: 0.8034 (tp) cc_final: 0.7749 (tp) REVERT: Y 21 MET cc_start: 0.7810 (tpp) cc_final: 0.7526 (tpp) outliers start: 33 outliers final: 29 residues processed: 200 average time/residue: 0.2721 time to fit residues: 70.7378 Evaluate side-chains 212 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG 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 154 SER 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 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 75 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 57 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.141814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125238 restraints weight = 11196.833| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.11 r_work: 0.3484 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8309 Z= 0.214 Angle : 0.562 8.391 11255 Z= 0.294 Chirality : 0.043 0.219 1263 Planarity : 0.004 0.059 1433 Dihedral : 4.692 38.842 1118 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.99 % Allowed : 18.47 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1007 helix: 1.87 (0.26), residues: 391 sheet: 0.00 (0.34), residues: 225 loop : -0.86 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.003 0.001 HIS B 266 PHE 0.015 0.001 PHE R 306 TYR 0.011 0.001 TYR N 32 ARG 0.013 0.000 ARG A 283 ********************** 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 214 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8291 (tptp) cc_final: 0.7922 (tptp) REVERT: A 220 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6295 (t70) REVERT: A 222 PHE cc_start: 0.7504 (m-80) cc_final: 0.6377 (m-80) REVERT: A 228 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7648 (ptm160) REVERT: A 350 THR cc_start: 0.8449 (m) cc_final: 0.8201 (p) REVERT: A 392 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7304 (mm-30) REVERT: B 46 ARG cc_start: 0.6684 (mpp-170) cc_final: 0.6403 (mpp-170) REVERT: B 67 SER cc_start: 0.8271 (m) cc_final: 0.8007 (p) REVERT: B 75 GLN cc_start: 0.7964 (mt0) cc_final: 0.7721 (mt0) REVERT: B 98 SER cc_start: 0.7970 (m) cc_final: 0.7684 (p) REVERT: B 118 ASP cc_start: 0.7269 (p0) cc_final: 0.6941 (p0) REVERT: B 134 ARG cc_start: 0.7511 (ptt90) cc_final: 0.7174 (ptt90) REVERT: B 135 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7632 (m) REVERT: B 153 ASP cc_start: 0.7583 (t0) cc_final: 0.7208 (t0) REVERT: B 212 ASP cc_start: 0.7538 (t0) cc_final: 0.7265 (t0) REVERT: B 219 ARG cc_start: 0.8320 (tpp80) cc_final: 0.7712 (mmt90) REVERT: B 253 PHE cc_start: 0.8565 (m-80) cc_final: 0.8017 (m-80) REVERT: B 277 SER cc_start: 0.8161 (t) cc_final: 0.7683 (p) REVERT: B 283 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7501 (ttt90) REVERT: B 298 ASP cc_start: 0.7422 (t70) cc_final: 0.7070 (t0) REVERT: B 300 LEU cc_start: 0.8151 (mt) cc_final: 0.7653 (mp) REVERT: B 316 SER cc_start: 0.7731 (t) cc_final: 0.7348 (p) REVERT: B 333 ASP cc_start: 0.7683 (p0) cc_final: 0.7384 (p0) REVERT: N 34 MET cc_start: 0.8164 (mmm) cc_final: 0.7880 (tpt) REVERT: R 279 ILE cc_start: 0.8073 (tp) cc_final: 0.7806 (tp) REVERT: Y 21 MET cc_start: 0.7787 (tpp) cc_final: 0.7501 (tpp) outliers start: 35 outliers final: 29 residues processed: 197 average time/residue: 0.2612 time to fit residues: 66.0611 Evaluate side-chains 211 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 79 LEU 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 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG 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 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 228 SER 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 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.0070 chunk 47 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 90 optimal weight: 0.0030 chunk 89 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 overall best weight: 0.0766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133230 restraints weight = 11355.875| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.15 r_work: 0.3541 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8309 Z= 0.124 Angle : 0.529 8.936 11255 Z= 0.276 Chirality : 0.041 0.209 1263 Planarity : 0.004 0.054 1433 Dihedral : 4.347 33.132 1118 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.85 % Allowed : 19.95 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 1007 helix: 2.08 (0.26), residues: 390 sheet: 0.14 (0.35), residues: 208 loop : -0.81 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.004 0.001 HIS R 124 PHE 0.014 0.001 PHE N 29 TYR 0.008 0.001 TYR B 59 ARG 0.014 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4669.58 seconds wall clock time: 81 minutes 7.49 seconds (4867.49 seconds total)