Starting phenix.real_space_refine on Fri Sep 11 10:40:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pb0_20284/09_2026/6pb0_20284.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pb0_20284/09_2026/6pb0_20284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pb0_20284/09_2026/6pb0_20284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pb0_20284/09_2026/6pb0_20284.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pb0_20284/09_2026/6pb0_20284.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pb0_20284/09_2026/6pb0_20284.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pb0_20284/09_2026/6pb0_20284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pb0_20284/09_2026/6pb0_20284.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 50 5.16 5 C 5685 2.51 5 N 1509 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8827 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2349 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain: "U" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "A" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1892 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: "R" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 266 Unusual residues: {'CLR': 5, 'PLM': 7} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 8827 At special positions: 0 Unit cell: (102.414, 98.358, 142.974, 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 50 16.00 O 1583 8.00 N 1509 7.00 C 5685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 309.7 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2014 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 42.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 112 through 144 removed outlier: 3.606A pdb=" N HIS R 117 " --> pdb=" O LYS R 113 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL R 118 " --> pdb=" O VAL R 114 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS R 128 " --> pdb=" O TYR R 124 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL R 136 " --> pdb=" O VAL R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 175 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.853A pdb=" N SER R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 218 removed outlier: 3.707A pdb=" N ARG R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 223 removed outlier: 3.554A pdb=" N THR R 223 " --> pdb=" O THR R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 236 removed outlier: 3.806A pdb=" N PHE R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 253 removed outlier: 3.906A pdb=" N ILE R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 260 removed outlier: 3.510A pdb=" N TRP R 259 " --> pdb=" O GLU R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 302 Proline residue: R 275 - end of helix removed outlier: 3.523A pdb=" N LEU R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU R 287 " --> pdb=" O ASN R 283 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA R 300 " --> pdb=" O THR R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 324 removed outlier: 3.557A pdb=" N GLN R 308 " --> pdb=" O SER R 304 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 339 through 365 removed outlier: 5.186A pdb=" N GLY R 356 " --> pdb=" O GLU R 352 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE R 357 " --> pdb=" O SER R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 386 Processing helix chain 'U' and resid 8 through 40 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.871A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.665A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 312' Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.062A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.814A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.912A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.509A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.786A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.560A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.000A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.697A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.088A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.616A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.489A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.716A 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: 3.851A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.583A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.032A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.097A 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: 6.716A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.18 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: 2734 1.34 - 1.46: 1951 1.46 - 1.58: 4264 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 9019 Sorted by residual: bond pdb=" C10 CLR R 402 " pdb=" C9 CLR R 402 " ideal model delta sigma weight residual 1.551 1.518 0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C5 CLR R 406 " pdb=" C6 CLR R 406 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C10 CLR R 404 " pdb=" C9 CLR R 404 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C10 CLR R 401 " pdb=" C9 CLR R 401 " ideal model delta sigma weight residual 1.551 1.521 0.030 2.00e-02 2.50e+03 2.25e+00 ... (remaining 9014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 11572 1.70 - 3.41: 508 3.41 - 5.11: 87 5.11 - 6.81: 22 6.81 - 8.52: 7 Bond angle restraints: 12196 Sorted by residual: angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" CA THR B 87 " pdb=" CB THR B 87 " pdb=" CG2 THR B 87 " ideal model delta sigma weight residual 110.50 115.65 -5.15 1.70e+00 3.46e-01 9.18e+00 angle pdb=" CA TYR R 272 " pdb=" CB TYR R 272 " pdb=" CG TYR R 272 " ideal model delta sigma weight residual 113.90 118.83 -4.93 1.80e+00 3.09e-01 7.51e+00 angle pdb=" C ILE R 271 " pdb=" N TYR R 272 " pdb=" CA TYR R 272 " ideal model delta sigma weight residual 122.26 117.60 4.66 1.73e+00 3.34e-01 7.24e+00 angle pdb=" CA LEU R 320 " pdb=" C LEU R 320 " pdb=" N PRO R 321 " ideal model delta sigma weight residual 118.44 122.69 -4.25 1.59e+00 3.96e-01 7.14e+00 ... (remaining 12191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.93: 5083 14.93 - 29.85: 191 29.85 - 44.78: 48 44.78 - 59.70: 11 59.70 - 74.63: 3 Dihedral angle restraints: 5336 sinusoidal: 2225 harmonic: 3111 Sorted by residual: dihedral pdb=" CA ALA R 133 " pdb=" C ALA R 133 " pdb=" N LEU R 134 " pdb=" CA LEU R 134 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA PHE R 284 " pdb=" C PHE R 284 " pdb=" N ILE R 285 " pdb=" CA ILE R 285 " ideal model delta harmonic sigma weight residual -180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA HIS R 115 " pdb=" C HIS R 115 " pdb=" N TYR R 116 " pdb=" CA TYR R 116 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1195 0.085 - 0.169: 134 0.169 - 0.254: 14 0.254 - 0.338: 3 0.338 - 0.423: 8 Chirality restraints: 1354 Sorted by residual: chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 1351 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 295 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET R 295 " 0.041 2.00e-02 2.50e+03 pdb=" O MET R 295 " -0.015 2.00e-02 2.50e+03 pdb=" N THR R 296 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 291 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C VAL R 291 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL R 291 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG R 292 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 288 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C PHE R 288 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE R 288 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN R 289 " -0.013 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2116 2.80 - 3.33: 7309 3.33 - 3.85: 13688 3.85 - 4.38: 15811 4.38 - 4.90: 28166 Nonbonded interactions: 67090 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.299 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.308 3.040 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.343 3.120 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.401 3.040 ... (remaining 67085 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 9022 Z= 0.193 Angle : 0.825 8.517 12202 Z= 0.432 Chirality : 0.063 0.423 1354 Planarity : 0.006 0.056 1517 Dihedral : 9.190 74.628 3313 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.22 % Allowed : 1.29 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.20), residues: 1050 helix: -1.43 (0.18), residues: 424 sheet: -1.35 (0.31), residues: 226 loop : -2.57 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 118 TYR 0.022 0.002 TYR N 94 PHE 0.024 0.002 PHE R 203 TRP 0.033 0.003 TRP R 156 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 ( 9019) covalent geometry : angle 0.82397 / 0.43 (12196) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 2.03465 / 1.12 ( 6) hydrogen bonds : bond 0.14245 / 9.38 ( 440) hydrogen bonds : angle 6.00809 / 4.19 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7354 (mtp85) cc_final: 0.6727 (tmt170) REVERT: U 24 GLN cc_start: 0.8159 (tp40) cc_final: 0.7800 (mt0) REVERT: A 218 ASN cc_start: 0.7579 (m-40) cc_final: 0.7345 (m110) REVERT: A 220 HIS cc_start: 0.6201 (t-90) cc_final: 0.5542 (t-90) REVERT: A 284 THR cc_start: 0.8124 (m) cc_final: 0.7844 (p) REVERT: B 189 SER cc_start: 0.8731 (p) cc_final: 0.8384 (m) REVERT: B 258 ASP cc_start: 0.7241 (t70) cc_final: 0.6486 (t0) outliers start: 2 outliers final: 0 residues processed: 258 average time/residue: 0.5195 time to fit residues: 143.3040 Evaluate side-chains 159 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 181 HIS R 182 GLN R 255 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.185187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.141917 restraints weight = 10980.283| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 3.08 r_work: 0.3762 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9022 Z= 0.121 Angle : 0.499 5.157 12202 Z= 0.265 Chirality : 0.041 0.131 1354 Planarity : 0.004 0.042 1517 Dihedral : 6.405 59.398 1317 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.88 % Allowed : 13.70 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.24), residues: 1050 helix: 1.20 (0.24), residues: 422 sheet: -1.03 (0.31), residues: 227 loop : -1.94 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 256 TYR 0.016 0.001 TYR N 60 PHE 0.015 0.001 PHE R 260 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9019) covalent geometry : angle 0.49782 / 0.26 (12196) SS BOND : bond 0.00385 / 0.19 ( 3) SS BOND : angle 1.27843 / 0.44 ( 6) hydrogen bonds : bond 0.04083 / 2.77 ( 440) hydrogen bonds : angle 4.26995 / 3.03 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 292 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7249 (ttp80) REVERT: R 309 TYR cc_start: 0.7380 (m-80) cc_final: 0.6363 (m-80) REVERT: R 377 ARG cc_start: 0.7445 (mtp85) cc_final: 0.6338 (tmt170) REVERT: A 217 VAL cc_start: 0.8370 (t) cc_final: 0.8120 (p) REVERT: A 218 ASN cc_start: 0.7790 (m-40) cc_final: 0.7513 (m110) REVERT: A 222 PHE cc_start: 0.8076 (m-80) cc_final: 0.7599 (m-80) REVERT: A 229 ASP cc_start: 0.6783 (t0) cc_final: 0.6520 (t0) REVERT: B 22 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7327 (ttm170) REVERT: B 189 SER cc_start: 0.8922 (p) cc_final: 0.8598 (m) REVERT: B 271 CYS cc_start: 0.8468 (m) cc_final: 0.7658 (p) REVERT: G 40 TYR cc_start: 0.8541 (t80) cc_final: 0.8329 (t80) outliers start: 36 outliers final: 16 residues processed: 194 average time/residue: 0.5025 time to fit residues: 104.9243 Evaluate side-chains 172 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 292 ARG Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain R residue 379 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 96 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 117 HIS R 182 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 6 GLN B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.176248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132312 restraints weight = 10922.450| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.06 r_work: 0.3637 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9022 Z= 0.171 Angle : 0.539 6.863 12202 Z= 0.284 Chirality : 0.042 0.162 1354 Planarity : 0.004 0.040 1517 Dihedral : 6.320 58.953 1317 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.42 % Allowed : 15.10 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1050 helix: 1.91 (0.25), residues: 424 sheet: -0.90 (0.32), residues: 217 loop : -1.66 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.018 0.001 TYR R 272 PHE 0.016 0.002 PHE A 212 TRP 0.022 0.002 TRP R 156 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 9019) covalent geometry : angle 0.53869 / 0.28 (12196) SS BOND : bond 0.00834 / 0.40 ( 3) SS BOND : angle 1.37394 / 0.50 ( 6) hydrogen bonds : bond 0.04622 / 3.14 ( 440) hydrogen bonds : angle 4.19400 / 2.97 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.301 Fit side-chains REVERT: R 309 TYR cc_start: 0.7467 (m-80) cc_final: 0.6871 (m-80) REVERT: R 317 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7081 (mm) REVERT: R 377 ARG cc_start: 0.7452 (mtp85) cc_final: 0.6290 (tmt170) REVERT: A 29 GLN cc_start: 0.7846 (tp40) cc_final: 0.6646 (tt0) REVERT: A 222 PHE cc_start: 0.8151 (m-80) cc_final: 0.7852 (m-80) REVERT: A 284 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 343 ASP cc_start: 0.7611 (t0) cc_final: 0.7221 (t0) REVERT: B 38 ASP cc_start: 0.7908 (t70) cc_final: 0.7548 (m-30) REVERT: B 42 ARG cc_start: 0.7840 (tpt90) cc_final: 0.7073 (ttt90) REVERT: B 156 GLN cc_start: 0.8213 (mt0) cc_final: 0.7636 (mt0) REVERT: B 175 GLN cc_start: 0.7950 (mt0) cc_final: 0.7541 (mm-40) REVERT: B 189 SER cc_start: 0.9023 (p) cc_final: 0.8682 (m) REVERT: B 254 ASP cc_start: 0.8363 (t70) cc_final: 0.8127 (t70) REVERT: B 258 ASP cc_start: 0.7931 (t70) cc_final: 0.7359 (t0) REVERT: B 271 CYS cc_start: 0.8621 (m) cc_final: 0.7913 (p) REVERT: G 40 TYR cc_start: 0.8672 (t80) cc_final: 0.8271 (t80) REVERT: N 110 VAL cc_start: 0.8911 (t) cc_final: 0.8705 (m) REVERT: N 120 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7299 (mt0) outliers start: 41 outliers final: 20 residues processed: 183 average time/residue: 0.4667 time to fit residues: 91.9830 Evaluate side-chains 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 339 VAL Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain R residue 379 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 24 GLN A 294 GLN B 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135134 restraints weight = 10991.900| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.09 r_work: 0.3671 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9022 Z= 0.099 Angle : 0.476 7.077 12202 Z= 0.252 Chirality : 0.040 0.163 1354 Planarity : 0.003 0.035 1517 Dihedral : 5.700 59.616 1317 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.31 % Allowed : 16.61 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1050 helix: 2.31 (0.25), residues: 428 sheet: -0.80 (0.33), residues: 215 loop : -1.50 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.013 0.001 TYR R 272 PHE 0.013 0.001 PHE R 260 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 9019) covalent geometry : angle 0.47146 / 0.25 (12196) SS BOND : bond 0.00574 / 0.29 ( 3) SS BOND : angle 2.90984 / 0.98 ( 6) hydrogen bonds : bond 0.03578 / 2.43 ( 440) hydrogen bonds : angle 3.90635 / 2.75 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: R 309 TYR cc_start: 0.7351 (m-80) cc_final: 0.6736 (m-80) REVERT: R 377 ARG cc_start: 0.7397 (mtp85) cc_final: 0.6300 (tmt170) REVERT: A 218 ASN cc_start: 0.7838 (m-40) cc_final: 0.7620 (m110) REVERT: A 222 PHE cc_start: 0.8192 (m-80) cc_final: 0.7809 (m-80) REVERT: A 230 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: A 284 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8307 (p) REVERT: A 331 ASP cc_start: 0.3827 (OUTLIER) cc_final: 0.3514 (m-30) REVERT: A 343 ASP cc_start: 0.7649 (t0) cc_final: 0.7238 (t0) REVERT: B 42 ARG cc_start: 0.7937 (tpt90) cc_final: 0.7085 (ttt90) REVERT: B 156 GLN cc_start: 0.8153 (mt0) cc_final: 0.7588 (mt0) REVERT: B 175 GLN cc_start: 0.7989 (mt0) cc_final: 0.7587 (mm-40) REVERT: B 189 SER cc_start: 0.9001 (p) cc_final: 0.8660 (m) REVERT: B 234 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: B 254 ASP cc_start: 0.8334 (t70) cc_final: 0.8127 (t70) REVERT: B 258 ASP cc_start: 0.7936 (t70) cc_final: 0.7334 (t0) REVERT: B 262 MET cc_start: 0.8399 (tpp) cc_final: 0.7412 (mmt) REVERT: B 271 CYS cc_start: 0.8566 (m) cc_final: 0.7883 (p) REVERT: G 40 TYR cc_start: 0.8615 (t80) cc_final: 0.8290 (t80) REVERT: N 110 VAL cc_start: 0.8938 (t) cc_final: 0.8728 (m) REVERT: N 120 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7335 (mt0) outliers start: 40 outliers final: 17 residues processed: 181 average time/residue: 0.4816 time to fit residues: 94.0380 Evaluate side-chains 167 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 379 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.0040 chunk 82 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 45 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.180165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136699 restraints weight = 10956.430| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.11 r_work: 0.3684 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9022 Z= 0.092 Angle : 0.458 5.979 12202 Z= 0.242 Chirality : 0.040 0.172 1354 Planarity : 0.003 0.035 1517 Dihedral : 5.441 59.053 1317 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.45 % Allowed : 17.69 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1050 helix: 2.70 (0.25), residues: 422 sheet: -0.65 (0.32), residues: 228 loop : -1.36 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 280 TYR 0.011 0.001 TYR N 60 PHE 0.013 0.001 PHE R 260 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 9019) covalent geometry : angle 0.45520 / 0.24 (12196) SS BOND : bond 0.00110 / 0.05 ( 3) SS BOND : angle 2.26396 / 0.77 ( 6) hydrogen bonds : bond 0.03261 / 2.20 ( 440) hydrogen bonds : angle 3.74049 / 2.65 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7335 (mtp85) cc_final: 0.6221 (tmt170) REVERT: A 209 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 217 VAL cc_start: 0.8381 (t) cc_final: 0.8115 (p) REVERT: A 218 ASN cc_start: 0.7854 (m-40) cc_final: 0.7626 (m110) REVERT: A 230 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7925 (mm-30) REVERT: A 284 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 343 ASP cc_start: 0.7653 (t0) cc_final: 0.7252 (t0) REVERT: B 42 ARG cc_start: 0.7927 (tpt90) cc_final: 0.7116 (ttt90) REVERT: B 156 GLN cc_start: 0.8141 (mt0) cc_final: 0.7567 (mt0) REVERT: B 175 GLN cc_start: 0.7873 (mt0) cc_final: 0.7487 (mm-40) REVERT: B 189 SER cc_start: 0.8909 (p) cc_final: 0.8553 (m) REVERT: B 234 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: B 254 ASP cc_start: 0.8377 (t70) cc_final: 0.8156 (t70) REVERT: B 258 ASP cc_start: 0.7899 (t70) cc_final: 0.7584 (t0) REVERT: B 262 MET cc_start: 0.8299 (tpp) cc_final: 0.7272 (mmt) REVERT: B 271 CYS cc_start: 0.8564 (m) cc_final: 0.7789 (p) REVERT: G 40 TYR cc_start: 0.8534 (t80) cc_final: 0.8239 (t80) REVERT: N 120 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7267 (mt0) outliers start: 32 outliers final: 16 residues processed: 179 average time/residue: 0.4596 time to fit residues: 89.0508 Evaluate side-chains 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 75 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.178712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135528 restraints weight = 10922.400| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.09 r_work: 0.3671 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9022 Z= 0.102 Angle : 0.469 5.967 12202 Z= 0.248 Chirality : 0.040 0.179 1354 Planarity : 0.003 0.037 1517 Dihedral : 5.377 58.589 1317 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.02 % Allowed : 18.45 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1050 helix: 2.83 (0.25), residues: 419 sheet: -0.54 (0.32), residues: 230 loop : -1.28 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 280 TYR 0.010 0.001 TYR R 272 PHE 0.013 0.001 PHE R 260 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 9019) covalent geometry : angle 0.46632 / 0.25 (12196) SS BOND : bond 0.00154 / 0.07 ( 3) SS BOND : angle 2.24801 / 0.76 ( 6) hydrogen bonds : bond 0.03361 / 2.28 ( 440) hydrogen bonds : angle 3.72877 / 2.64 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: R 182 GLN cc_start: 0.8281 (tp-100) cc_final: 0.8035 (tm-30) REVERT: R 377 ARG cc_start: 0.7262 (mtp85) cc_final: 0.6194 (tmt170) REVERT: A 217 VAL cc_start: 0.8400 (t) cc_final: 0.8152 (m) REVERT: A 230 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: A 265 ARG cc_start: 0.7415 (mmm160) cc_final: 0.7146 (mtp85) REVERT: A 284 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 331 ASP cc_start: 0.3678 (OUTLIER) cc_final: 0.3371 (m-30) REVERT: A 343 ASP cc_start: 0.7657 (t0) cc_final: 0.7259 (t0) REVERT: B 22 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7307 (mmt90) REVERT: B 42 ARG cc_start: 0.7936 (tpt90) cc_final: 0.7124 (ttt90) REVERT: B 59 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: B 156 GLN cc_start: 0.8259 (mt0) cc_final: 0.7655 (mt0) REVERT: B 175 GLN cc_start: 0.7841 (mt0) cc_final: 0.7450 (mm-40) REVERT: B 189 SER cc_start: 0.8973 (p) cc_final: 0.8621 (m) REVERT: B 234 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 239 ASN cc_start: 0.8292 (m-40) cc_final: 0.8079 (m110) REVERT: B 254 ASP cc_start: 0.8335 (t70) cc_final: 0.8125 (t70) REVERT: B 258 ASP cc_start: 0.7703 (t70) cc_final: 0.7049 (t0) REVERT: B 262 MET cc_start: 0.8284 (tpp) cc_final: 0.7236 (mmt) REVERT: B 271 CYS cc_start: 0.8532 (m) cc_final: 0.7806 (p) REVERT: G 40 TYR cc_start: 0.8585 (t80) cc_final: 0.8265 (t80) REVERT: N 120 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7278 (mt0) outliers start: 28 outliers final: 20 residues processed: 164 average time/residue: 0.4834 time to fit residues: 85.4893 Evaluate side-chains 165 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain R residue 379 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 382 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.176471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133022 restraints weight = 10991.804| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.09 r_work: 0.3640 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9022 Z= 0.122 Angle : 0.485 5.699 12202 Z= 0.256 Chirality : 0.041 0.189 1354 Planarity : 0.003 0.038 1517 Dihedral : 5.510 58.044 1317 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.78 % Allowed : 17.91 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1050 helix: 2.97 (0.25), residues: 413 sheet: -0.47 (0.31), residues: 234 loop : -1.23 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 280 TYR 0.010 0.001 TYR R 363 PHE 0.016 0.001 PHE A 222 TRP 0.015 0.001 TRP B 99 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 9019) covalent geometry : angle 0.48216 / 0.25 (12196) SS BOND : bond 0.00189 / 0.09 ( 3) SS BOND : angle 2.27006 / 0.77 ( 6) hydrogen bonds : bond 0.03656 / 2.48 ( 440) hydrogen bonds : angle 3.82213 / 2.71 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6225 (tmt170) REVERT: U 8 ASP cc_start: 0.7085 (t70) cc_final: 0.6879 (t70) REVERT: A 217 VAL cc_start: 0.8422 (t) cc_final: 0.8156 (p) REVERT: A 230 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: A 265 ARG cc_start: 0.7442 (mmm160) cc_final: 0.7007 (mtp85) REVERT: A 284 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 331 ASP cc_start: 0.3664 (OUTLIER) cc_final: 0.3315 (m-30) REVERT: A 343 ASP cc_start: 0.7639 (t0) cc_final: 0.7253 (t0) REVERT: B 42 ARG cc_start: 0.7952 (tpt90) cc_final: 0.7143 (ttt90) REVERT: B 59 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: B 156 GLN cc_start: 0.8332 (mt0) cc_final: 0.7683 (mt0) REVERT: B 175 GLN cc_start: 0.7843 (mt0) cc_final: 0.7456 (mm-40) REVERT: B 189 SER cc_start: 0.8976 (p) cc_final: 0.8627 (m) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: B 254 ASP cc_start: 0.8307 (t70) cc_final: 0.8069 (t0) REVERT: B 262 MET cc_start: 0.8326 (tpp) cc_final: 0.7245 (mmt) REVERT: B 271 CYS cc_start: 0.8604 (m) cc_final: 0.7856 (p) REVERT: B 325 MET cc_start: 0.7648 (mmt) cc_final: 0.7312 (mmt) REVERT: G 40 TYR cc_start: 0.8579 (t80) cc_final: 0.8216 (t80) REVERT: N 38 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7143 (ptp90) REVERT: N 120 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7263 (mt0) outliers start: 35 outliers final: 21 residues processed: 172 average time/residue: 0.5244 time to fit residues: 96.8708 Evaluate side-chains 165 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 97 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.172203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133294 restraints weight = 10771.220| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.80 r_work: 0.3640 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9022 Z= 0.130 Angle : 0.499 6.142 12202 Z= 0.262 Chirality : 0.041 0.190 1354 Planarity : 0.003 0.038 1517 Dihedral : 5.585 57.494 1317 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.24 % Allowed : 19.09 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1050 helix: 2.83 (0.25), residues: 419 sheet: -0.42 (0.32), residues: 226 loop : -1.28 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 280 TYR 0.010 0.001 TYR R 363 PHE 0.014 0.001 PHE R 260 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9019) covalent geometry : angle 0.49626 / 0.26 (12196) SS BOND : bond 0.00167 / 0.08 ( 3) SS BOND : angle 2.22109 / 0.75 ( 6) hydrogen bonds : bond 0.03746 / 2.54 ( 440) hydrogen bonds : angle 3.87559 / 2.75 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7276 (mtp85) cc_final: 0.6195 (tmt170) REVERT: A 217 VAL cc_start: 0.8416 (t) cc_final: 0.8142 (p) REVERT: A 230 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: A 265 ARG cc_start: 0.7439 (mmm160) cc_final: 0.7183 (mtp85) REVERT: A 284 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8448 (p) REVERT: A 331 ASP cc_start: 0.3637 (OUTLIER) cc_final: 0.3269 (m-30) REVERT: A 343 ASP cc_start: 0.7601 (t0) cc_final: 0.7243 (t0) REVERT: B 42 ARG cc_start: 0.7928 (tpt90) cc_final: 0.7141 (ttt90) REVERT: B 59 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: B 175 GLN cc_start: 0.7827 (mt0) cc_final: 0.7459 (mm-40) REVERT: B 189 SER cc_start: 0.8977 (p) cc_final: 0.8626 (m) REVERT: B 234 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8711 (m-80) REVERT: B 271 CYS cc_start: 0.8595 (m) cc_final: 0.7888 (p) REVERT: B 298 ASP cc_start: 0.8496 (t0) cc_final: 0.8185 (t0) REVERT: G 40 TYR cc_start: 0.8585 (t80) cc_final: 0.8209 (t80) REVERT: N 38 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7095 (ptp90) REVERT: N 110 VAL cc_start: 0.8994 (t) cc_final: 0.8775 (m) REVERT: N 120 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7282 (mt0) outliers start: 30 outliers final: 18 residues processed: 160 average time/residue: 0.5129 time to fit residues: 88.0221 Evaluate side-chains 160 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 79 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.177709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134346 restraints weight = 10921.563| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.08 r_work: 0.3658 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9022 Z= 0.106 Angle : 0.486 5.851 12202 Z= 0.256 Chirality : 0.040 0.198 1354 Planarity : 0.003 0.039 1517 Dihedral : 5.441 56.586 1317 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.13 % Allowed : 19.63 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1050 helix: 3.03 (0.25), residues: 413 sheet: -0.31 (0.33), residues: 219 loop : -1.23 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 280 TYR 0.009 0.001 TYR R 272 PHE 0.014 0.001 PHE R 260 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9019) covalent geometry : angle 0.48388 / 0.26 (12196) SS BOND : bond 0.00226 / 0.11 ( 3) SS BOND : angle 2.15334 / 0.73 ( 6) hydrogen bonds : bond 0.03454 / 2.34 ( 440) hydrogen bonds : angle 3.80120 / 2.70 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7270 (mtp85) cc_final: 0.6179 (tmt170) REVERT: A 217 VAL cc_start: 0.8369 (t) cc_final: 0.8088 (p) REVERT: A 230 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: A 265 ARG cc_start: 0.7378 (mmm160) cc_final: 0.7117 (mtp85) REVERT: A 284 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8490 (p) REVERT: A 331 ASP cc_start: 0.3574 (OUTLIER) cc_final: 0.3222 (m-30) REVERT: A 343 ASP cc_start: 0.7610 (t0) cc_final: 0.7231 (t0) REVERT: B 42 ARG cc_start: 0.7938 (tpt90) cc_final: 0.7134 (ttt90) REVERT: B 59 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: B 175 GLN cc_start: 0.7836 (mt0) cc_final: 0.7440 (mm-40) REVERT: B 189 SER cc_start: 0.8967 (p) cc_final: 0.8610 (m) REVERT: B 234 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: B 254 ASP cc_start: 0.8183 (t70) cc_final: 0.7982 (t70) REVERT: B 262 MET cc_start: 0.8222 (tpp) cc_final: 0.7289 (mmt) REVERT: B 271 CYS cc_start: 0.8583 (m) cc_final: 0.7855 (p) REVERT: B 298 ASP cc_start: 0.8534 (t0) cc_final: 0.8233 (t0) REVERT: G 40 TYR cc_start: 0.8565 (t80) cc_final: 0.8206 (t80) REVERT: N 38 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7124 (ptp90) REVERT: N 120 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7203 (mt0) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 0.5043 time to fit residues: 87.8907 Evaluate side-chains 162 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 339 VAL Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.173756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135113 restraints weight = 10661.711| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.78 r_work: 0.3661 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9022 Z= 0.111 Angle : 0.496 6.629 12202 Z= 0.261 Chirality : 0.041 0.237 1354 Planarity : 0.003 0.039 1517 Dihedral : 5.424 56.441 1317 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.13 % Allowed : 19.63 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.26), residues: 1050 helix: 3.05 (0.25), residues: 413 sheet: -0.30 (0.33), residues: 221 loop : -1.22 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 347 TYR 0.009 0.001 TYR R 272 PHE 0.017 0.001 PHE A 222 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9019) covalent geometry : angle 0.49338 / 0.26 (12196) SS BOND : bond 0.00205 / 0.10 ( 3) SS BOND : angle 2.31180 / 0.78 ( 6) hydrogen bonds : bond 0.03492 / 2.36 ( 440) hydrogen bonds : angle 3.80664 / 2.70 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: R 118 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8168 (p) REVERT: R 377 ARG cc_start: 0.7277 (mtp85) cc_final: 0.6195 (tmt170) REVERT: A 29 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7120 (tp-100) REVERT: A 217 VAL cc_start: 0.8373 (t) cc_final: 0.8093 (p) REVERT: A 230 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: A 284 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8476 (p) REVERT: A 343 ASP cc_start: 0.7604 (t0) cc_final: 0.7235 (t0) REVERT: B 42 ARG cc_start: 0.7943 (tpt90) cc_final: 0.7146 (ttt90) REVERT: B 59 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: B 175 GLN cc_start: 0.7784 (mt0) cc_final: 0.7413 (mm-40) REVERT: B 189 SER cc_start: 0.8955 (p) cc_final: 0.8609 (m) REVERT: B 234 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: B 254 ASP cc_start: 0.8123 (t70) cc_final: 0.7914 (t70) REVERT: B 262 MET cc_start: 0.8139 (tpp) cc_final: 0.7241 (mmt) REVERT: B 271 CYS cc_start: 0.8566 (m) cc_final: 0.7860 (p) REVERT: B 298 ASP cc_start: 0.8504 (t0) cc_final: 0.8205 (t0) REVERT: G 40 TYR cc_start: 0.8607 (t80) cc_final: 0.8265 (t80) REVERT: N 38 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7099 (ptp90) REVERT: N 52 SER cc_start: 0.8625 (m) cc_final: 0.8265 (t) outliers start: 29 outliers final: 21 residues processed: 162 average time/residue: 0.5019 time to fit residues: 87.7002 Evaluate side-chains 165 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 339 VAL Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain R residue 379 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 90 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 295 ASN N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.176778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.138535 restraints weight = 10614.603| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.76 r_work: 0.3711 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9022 Z= 0.093 Angle : 0.474 7.923 12202 Z= 0.250 Chirality : 0.040 0.270 1354 Planarity : 0.003 0.040 1517 Dihedral : 5.164 58.931 1317 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.37 % Allowed : 20.82 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.26), residues: 1050 helix: 3.05 (0.25), residues: 419 sheet: -0.27 (0.33), residues: 215 loop : -1.20 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.013 0.001 TYR N 60 PHE 0.014 0.001 PHE R 260 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS R 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 ( 9019) covalent geometry : angle 0.47240 / 0.25 (12196) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 1.85247 / 0.63 ( 6) hydrogen bonds : bond 0.03100 / 2.10 ( 440) hydrogen bonds : angle 3.69204 / 2.62 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2982.45 seconds wall clock time: 51 minutes 32.84 seconds (3092.84 seconds total)