Starting phenix.real_space_refine on Thu Feb 13 13:53:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pb0_20284/02_2025/6pb0_20284.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pb0_20284/02_2025/6pb0_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_20284/02_2025/6pb0_20284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pb0_20284/02_2025/6pb0_20284.map" model { file = "/net/cci-nas-00/data/ceres_data/6pb0_20284/02_2025/6pb0_20284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pb0_20284/02_2025/6pb0_20284.cif" } resolution = 3.0 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= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.39, per 1000 atoms: 0.61 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: 2.41 Conformation dependent library (CDL) restraints added in 975.7 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: 1.03 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: 2.58 Time building geometry restraints manager: 2.75 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: 5339 14.93 - 29.85: 198 29.85 - 44.78: 60 44.78 - 59.70: 16 59.70 - 74.63: 3 Dihedral angle restraints: 5616 sinusoidal: 2505 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 5613 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: 0.800 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.810 Find NCS groups from input model: 0.090 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 9019 Z= 0.238 Angle : 0.824 8.517 12196 Z= 0.432 Chirality : 0.063 0.423 1354 Planarity : 0.006 0.056 1517 Dihedral : 9.455 74.628 3593 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.29 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 (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: -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 TRP 0.033 0.003 TRP R 156 HIS 0.010 0.001 HIS A 220 PHE 0.024 0.002 PHE R 203 TYR 0.022 0.002 TYR N 94 ARG 0.008 0.001 ARG N 118 *********************** 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 : 1.008 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: 0.8125 (m) cc_final: 0.7844 (p) REVERT: B 189 SER cc_start: 0.8732 (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: 1.1657 time to fit residues: 321.4412 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 : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 31 optimal weight: 0.0270 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS R 182 GLN R 255 ASN ** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4316 r_free = 0.4316 target = 0.184857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.141562 restraints weight = 10923.740| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.08 r_work: 0.3757 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9019 Z= 0.184 Angle : 0.502 5.333 12196 Z= 0.267 Chirality : 0.041 0.132 1354 Planarity : 0.004 0.041 1517 Dihedral : 7.449 59.240 1597 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.78 % Allowed : 13.81 % 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 (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: -0.72 (0.24), residues: 1050 helix: 1.19 (0.24), residues: 422 sheet: -1.03 (0.31), residues: 227 loop : -1.95 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 260 TYR 0.016 0.001 TYR N 60 ARG 0.009 0.001 ARG B 256 *********************** 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 211 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 292 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7245 (ttp80) REVERT: R 309 TYR cc_start: 0.7367 (m-80) cc_final: 0.6360 (m-80) REVERT: R 377 ARG cc_start: 0.7439 (mtp85) cc_final: 0.6329 (tmt170) REVERT: A 217 VAL cc_start: 0.8373 (t) cc_final: 0.8124 (p) REVERT: A 218 ASN cc_start: 0.7790 (m-40) cc_final: 0.7514 (m110) REVERT: A 222 PHE cc_start: 0.8074 (m-80) cc_final: 0.7592 (m-80) REVERT: A 229 ASP cc_start: 0.6781 (t0) cc_final: 0.6518 (t0) REVERT: B 22 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7346 (ttm170) REVERT: B 189 SER cc_start: 0.8853 (p) cc_final: 0.8595 (m) REVERT: B 271 CYS cc_start: 0.8478 (m) cc_final: 0.7678 (p) REVERT: G 40 TYR cc_start: 0.8538 (t80) cc_final: 0.8313 (t80) outliers start: 35 outliers final: 17 residues processed: 192 average time/residue: 1.0966 time to fit residues: 226.2121 Evaluate side-chains 174 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 67 SER 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 117 HIS R 182 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129780 restraints weight = 11084.528| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.06 r_work: 0.3606 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9019 Z= 0.335 Angle : 0.577 6.996 12196 Z= 0.305 Chirality : 0.044 0.143 1354 Planarity : 0.004 0.062 1517 Dihedral : 7.700 59.410 1597 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.75 % Allowed : 14.56 % Favored : 80.69 % 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: -0.13 (0.25), residues: 1050 helix: 1.79 (0.25), residues: 424 sheet: -0.92 (0.32), residues: 225 loop : -1.65 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 156 HIS 0.009 0.002 HIS A 220 PHE 0.017 0.002 PHE R 331 TYR 0.017 0.002 TYR N 94 ARG 0.008 0.001 ARG B 68 *********************** 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 203 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.839 Fit side-chains REVERT: R 377 ARG cc_start: 0.7404 (mtp85) cc_final: 0.6314 (tmt170) REVERT: A 284 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8344 (p) REVERT: A 343 ASP cc_start: 0.7591 (t0) cc_final: 0.7207 (t0) REVERT: B 42 ARG cc_start: 0.7830 (tpt90) cc_final: 0.7212 (ttt-90) REVERT: B 156 GLN cc_start: 0.8295 (mt0) cc_final: 0.7711 (mt0) REVERT: B 175 GLN cc_start: 0.7950 (mt0) cc_final: 0.7573 (mm-40) REVERT: B 234 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 258 ASP cc_start: 0.8002 (t70) cc_final: 0.7461 (t0) REVERT: B 271 CYS cc_start: 0.8634 (m) cc_final: 0.7981 (p) REVERT: G 40 TYR cc_start: 0.8644 (t80) cc_final: 0.8238 (t80) REVERT: N 120 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7346 (mt0) outliers start: 44 outliers final: 20 residues processed: 185 average time/residue: 1.0676 time to fit residues: 212.3210 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 78 LYS 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 B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL 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 71 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.176029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133088 restraints weight = 10887.522| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.01 r_work: 0.3656 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9019 Z= 0.185 Angle : 0.492 6.989 12196 Z= 0.262 Chirality : 0.041 0.166 1354 Planarity : 0.004 0.036 1517 Dihedral : 7.097 59.874 1597 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.81 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 (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: 0.28 (0.26), residues: 1050 helix: 2.24 (0.25), residues: 422 sheet: -0.84 (0.32), residues: 218 loop : -1.46 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.014 0.001 PHE R 260 TYR 0.011 0.001 TYR N 94 ARG 0.008 0.000 ARG A 347 *********************** 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 184 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7402 (mtp85) cc_final: 0.6281 (tmt170) REVERT: A 222 PHE cc_start: 0.8356 (m-80) cc_final: 0.8100 (m-10) REVERT: A 230 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: A 284 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 331 ASP cc_start: 0.4328 (OUTLIER) cc_final: 0.4015 (m-30) REVERT: A 343 ASP cc_start: 0.7665 (t0) cc_final: 0.7295 (t0) REVERT: B 42 ARG cc_start: 0.7903 (tpt90) cc_final: 0.7087 (ttt90) REVERT: B 156 GLN cc_start: 0.8228 (mt0) cc_final: 0.7640 (mt0) REVERT: B 175 GLN cc_start: 0.7939 (mt0) cc_final: 0.7542 (mm-40) REVERT: B 189 SER cc_start: 0.8989 (p) cc_final: 0.8507 (m) REVERT: B 234 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: B 258 ASP cc_start: 0.7961 (t70) cc_final: 0.7367 (t0) REVERT: B 262 MET cc_start: 0.8390 (tpp) cc_final: 0.7386 (mmt) REVERT: B 271 CYS cc_start: 0.8589 (m) cc_final: 0.7969 (p) REVERT: G 40 TYR cc_start: 0.8658 (t80) cc_final: 0.8273 (t80) REVERT: N 120 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7413 (mt0) outliers start: 40 outliers final: 19 residues processed: 166 average time/residue: 1.1032 time to fit residues: 196.8225 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 118 VAL Chi-restraints excluded: chain R residue 120 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 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 234 PHE Chi-restraints excluded: chain G residue 38 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.176413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133451 restraints weight = 10819.131| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.04 r_work: 0.3642 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9019 Z= 0.158 Angle : 0.470 6.255 12196 Z= 0.250 Chirality : 0.040 0.169 1354 Planarity : 0.003 0.040 1517 Dihedral : 6.764 59.323 1597 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.78 % Allowed : 16.94 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1050 helix: 2.56 (0.25), residues: 419 sheet: -0.72 (0.32), residues: 220 loop : -1.37 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE R 260 TYR 0.010 0.001 TYR N 60 ARG 0.007 0.000 ARG A 280 *********************** 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 179 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: R 182 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7811 (tp-100) REVERT: R 377 ARG cc_start: 0.7335 (mtp85) cc_final: 0.6229 (tmt170) REVERT: A 217 VAL cc_start: 0.8388 (t) cc_final: 0.8123 (p) REVERT: A 230 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: A 284 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 331 ASP cc_start: 0.3689 (OUTLIER) cc_final: 0.3392 (m-30) REVERT: A 343 ASP cc_start: 0.7615 (t0) cc_final: 0.7222 (t0) REVERT: B 42 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7079 (ttt90) REVERT: B 59 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: B 175 GLN cc_start: 0.7919 (mt0) cc_final: 0.7479 (mm-40) REVERT: B 189 SER cc_start: 0.9001 (p) cc_final: 0.8523 (m) REVERT: B 234 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: B 258 ASP cc_start: 0.7855 (t70) cc_final: 0.7275 (t0) REVERT: B 262 MET cc_start: 0.8329 (tpp) cc_final: 0.7237 (mmt) REVERT: B 271 CYS cc_start: 0.8580 (m) cc_final: 0.7875 (p) REVERT: G 40 TYR cc_start: 0.8610 (t80) cc_final: 0.8282 (t80) REVERT: N 38 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7116 (ptp90) REVERT: N 120 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7382 (mt0) outliers start: 35 outliers final: 21 residues processed: 165 average time/residue: 1.0536 time to fit residues: 187.2745 Evaluate side-chains 162 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 SER 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 266 VAL 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 29 GLN 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 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 0.0170 chunk 2 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.175856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132735 restraints weight = 10856.504| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.05 r_work: 0.3629 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9019 Z= 0.177 Angle : 0.481 8.318 12196 Z= 0.254 Chirality : 0.041 0.175 1354 Planarity : 0.003 0.042 1517 Dihedral : 6.654 58.903 1597 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.56 % Allowed : 17.58 % 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 (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: 0.70 (0.26), residues: 1050 helix: 2.66 (0.25), residues: 419 sheet: -0.57 (0.32), residues: 222 loop : -1.31 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE R 260 TYR 0.010 0.001 TYR R 363 ARG 0.007 0.000 ARG A 280 *********************** 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 170 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: R 182 GLN cc_start: 0.8316 (tp-100) cc_final: 0.8051 (tm-30) REVERT: R 377 ARG cc_start: 0.7252 (mtp85) cc_final: 0.6145 (tmt170) REVERT: A 217 VAL cc_start: 0.8397 (t) cc_final: 0.8133 (p) REVERT: A 230 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: A 265 ARG cc_start: 0.7359 (mmm160) cc_final: 0.7049 (mtp85) REVERT: A 284 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 331 ASP cc_start: 0.3747 (OUTLIER) cc_final: 0.3443 (m-30) REVERT: A 343 ASP cc_start: 0.7613 (t0) cc_final: 0.7224 (t0) REVERT: B 42 ARG cc_start: 0.7922 (tpt90) cc_final: 0.7109 (ttt90) REVERT: B 59 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: B 175 GLN cc_start: 0.7931 (mt0) cc_final: 0.7475 (mm-40) REVERT: B 189 SER cc_start: 0.9021 (p) cc_final: 0.8555 (m) REVERT: B 234 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: B 258 ASP cc_start: 0.7854 (t70) cc_final: 0.7268 (t0) REVERT: B 271 CYS cc_start: 0.8596 (m) cc_final: 0.7879 (p) REVERT: G 40 TYR cc_start: 0.8604 (t80) cc_final: 0.8196 (t80) REVERT: N 38 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7125 (ptp90) REVERT: N 120 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7385 (mt0) outliers start: 33 outliers final: 22 residues processed: 157 average time/residue: 1.1044 time to fit residues: 186.6022 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 SER 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 266 VAL 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 78 LYS Chi-restraints excluded: chain B residue 114 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 14 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.176325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135925 restraints weight = 10712.465| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.90 r_work: 0.3662 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9019 Z= 0.139 Angle : 0.458 7.029 12196 Z= 0.243 Chirality : 0.040 0.175 1354 Planarity : 0.003 0.042 1517 Dihedral : 6.346 57.990 1597 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.80 % Allowed : 18.77 % Favored : 78.43 % 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: 0.95 (0.26), residues: 1050 helix: 2.95 (0.25), residues: 413 sheet: -0.40 (0.33), residues: 217 loop : -1.24 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 99 HIS 0.010 0.001 HIS A 220 PHE 0.015 0.001 PHE R 260 TYR 0.009 0.001 TYR N 60 ARG 0.007 0.000 ARG A 280 *********************** 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 162 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: R 182 GLN cc_start: 0.8230 (tp-100) cc_final: 0.8016 (tm-30) REVERT: R 377 ARG cc_start: 0.7228 (mtp85) cc_final: 0.6140 (tmt170) REVERT: A 211 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8079 (mmtp) REVERT: A 217 VAL cc_start: 0.8397 (t) cc_final: 0.8107 (p) REVERT: A 230 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: A 265 ARG cc_start: 0.7321 (mmm160) cc_final: 0.7027 (mtp85) REVERT: A 284 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 331 ASP cc_start: 0.3659 (OUTLIER) cc_final: 0.3340 (m-30) REVERT: A 343 ASP cc_start: 0.7595 (t0) cc_final: 0.7208 (t0) REVERT: B 42 ARG cc_start: 0.7936 (tpt90) cc_final: 0.7125 (ttt90) REVERT: B 59 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: B 175 GLN cc_start: 0.7821 (mt0) cc_final: 0.7442 (mm-40) REVERT: B 189 SER cc_start: 0.8997 (p) cc_final: 0.8547 (m) REVERT: B 234 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: B 239 ASN cc_start: 0.8243 (m-40) cc_final: 0.7986 (m110) REVERT: B 258 ASP cc_start: 0.7824 (t70) cc_final: 0.7267 (t0) REVERT: B 262 MET cc_start: 0.8155 (tpp) cc_final: 0.7141 (mmt) REVERT: B 271 CYS cc_start: 0.8577 (m) cc_final: 0.7869 (p) REVERT: G 40 TYR cc_start: 0.8599 (t80) cc_final: 0.8274 (t80) REVERT: N 38 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7893 (ptt180) REVERT: N 120 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7277 (mt0) outliers start: 26 outliers final: 16 residues processed: 153 average time/residue: 1.0614 time to fit residues: 175.1657 Evaluate side-chains 155 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 SER 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 379 HIS 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 78 LYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE 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 79 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.170402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129706 restraints weight = 10895.842| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.90 r_work: 0.3597 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9019 Z= 0.297 Angle : 0.546 5.930 12196 Z= 0.288 Chirality : 0.043 0.190 1354 Planarity : 0.004 0.043 1517 Dihedral : 6.998 58.183 1597 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.21 % Allowed : 17.58 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 0.76 (0.26), residues: 1050 helix: 2.60 (0.25), residues: 421 sheet: -0.40 (0.32), residues: 222 loop : -1.25 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 99 HIS 0.010 0.001 HIS A 220 PHE 0.015 0.002 PHE R 344 TYR 0.013 0.001 TYR A 339 ARG 0.008 0.000 ARG A 280 *********************** 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 180 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.038 Fit side-chains REVERT: R 377 ARG cc_start: 0.7349 (mtp85) cc_final: 0.6246 (tmt170) REVERT: U 8 ASP cc_start: 0.7262 (t70) cc_final: 0.6984 (t70) REVERT: A 217 VAL cc_start: 0.8427 (t) cc_final: 0.8196 (p) REVERT: A 221 MET cc_start: 0.7942 (tpt) cc_final: 0.6688 (tpt) REVERT: A 230 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8133 (mm-30) REVERT: A 265 ARG cc_start: 0.7420 (mmm160) cc_final: 0.7124 (mtp85) REVERT: A 284 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 343 ASP cc_start: 0.7647 (t0) cc_final: 0.7305 (t0) REVERT: B 42 ARG cc_start: 0.7964 (tpt90) cc_final: 0.7124 (ttt90) REVERT: B 156 GLN cc_start: 0.8299 (mt0) cc_final: 0.7636 (mt0) REVERT: B 175 GLN cc_start: 0.7822 (mt0) cc_final: 0.7404 (mm-40) REVERT: B 234 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8777 (m-80) REVERT: B 258 ASP cc_start: 0.7986 (t70) cc_final: 0.7440 (t0) REVERT: B 262 MET cc_start: 0.8297 (tpp) cc_final: 0.7255 (mmt) REVERT: B 271 CYS cc_start: 0.8638 (m) cc_final: 0.7988 (p) REVERT: G 40 TYR cc_start: 0.8668 (t80) cc_final: 0.8176 (t80) REVERT: N 38 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7139 (ptp90) REVERT: N 80 TYR cc_start: 0.6668 (m-80) cc_final: 0.6119 (m-80) REVERT: N 120 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7441 (mt0) outliers start: 39 outliers final: 26 residues processed: 166 average time/residue: 1.0803 time to fit residues: 192.8888 Evaluate side-chains 163 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 SER 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 244 VAL Chi-restraints excluded: chain R residue 266 VAL 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 59 TYR 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 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER 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 83 MET 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 37 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.175453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132069 restraints weight = 10925.922| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.06 r_work: 0.3620 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9019 Z= 0.179 Angle : 0.497 5.806 12196 Z= 0.262 Chirality : 0.041 0.219 1354 Planarity : 0.003 0.043 1517 Dihedral : 6.642 57.087 1597 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.34 % Allowed : 18.77 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 0.89 (0.26), residues: 1050 helix: 2.81 (0.25), residues: 419 sheet: -0.38 (0.32), residues: 222 loop : -1.27 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.015 0.001 TYR N 60 ARG 0.008 0.000 ARG A 280 *********************** 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 162 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7337 (mtp85) cc_final: 0.6226 (tmt170) REVERT: U 8 ASP cc_start: 0.7043 (t70) cc_final: 0.6840 (t70) REVERT: A 217 VAL cc_start: 0.8388 (t) cc_final: 0.8123 (p) REVERT: A 230 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8080 (mm-30) REVERT: A 265 ARG cc_start: 0.7324 (mmm160) cc_final: 0.7047 (mtp85) REVERT: A 284 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (p) REVERT: A 343 ASP cc_start: 0.7624 (t0) cc_final: 0.7262 (t0) REVERT: B 42 ARG cc_start: 0.7951 (tpt90) cc_final: 0.7099 (ttt90) REVERT: B 59 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: B 175 GLN cc_start: 0.7822 (mt0) cc_final: 0.7386 (mm-40) REVERT: B 234 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8830 (m-80) REVERT: B 239 ASN cc_start: 0.8256 (m-40) cc_final: 0.7989 (m110) REVERT: B 258 ASP cc_start: 0.7894 (t70) cc_final: 0.7345 (t0) REVERT: B 271 CYS cc_start: 0.8597 (m) cc_final: 0.7932 (p) REVERT: G 40 TYR cc_start: 0.8618 (t80) cc_final: 0.8242 (t80) REVERT: N 38 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7165 (ptp90) REVERT: N 120 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7415 (mt0) outliers start: 31 outliers final: 22 residues processed: 151 average time/residue: 1.0926 time to fit residues: 177.4162 Evaluate side-chains 154 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 379 HIS 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 78 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 94 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.175421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132033 restraints weight = 10937.900| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.06 r_work: 0.3613 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9019 Z= 0.193 Angle : 0.511 6.623 12196 Z= 0.268 Chirality : 0.042 0.238 1354 Planarity : 0.004 0.044 1517 Dihedral : 6.601 56.706 1597 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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 : 3.57 % 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: 0.93 (0.26), residues: 1050 helix: 2.85 (0.25), residues: 419 sheet: -0.35 (0.32), residues: 222 loop : -1.26 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE R 260 TYR 0.009 0.001 TYR A 339 ARG 0.010 0.000 ARG A 347 ********************** 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 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7318 (mtp85) cc_final: 0.6119 (tpt90) REVERT: A 217 VAL cc_start: 0.8382 (t) cc_final: 0.8106 (p) REVERT: A 230 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: A 265 ARG cc_start: 0.7314 (mmm160) cc_final: 0.7047 (mtp85) REVERT: A 284 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 343 ASP cc_start: 0.7638 (t0) cc_final: 0.7267 (t0) REVERT: B 42 ARG cc_start: 0.7966 (tpt90) cc_final: 0.7111 (ttt90) REVERT: B 175 GLN cc_start: 0.7825 (mt0) cc_final: 0.7321 (mm-40) REVERT: B 234 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: B 239 ASN cc_start: 0.8287 (m-40) cc_final: 0.8070 (m110) REVERT: B 258 ASP cc_start: 0.7941 (t70) cc_final: 0.7385 (t0) REVERT: B 262 MET cc_start: 0.8176 (tpp) cc_final: 0.7166 (mmt) REVERT: B 271 CYS cc_start: 0.8614 (m) cc_final: 0.7925 (p) REVERT: G 40 TYR cc_start: 0.8606 (t80) cc_final: 0.8223 (t80) REVERT: N 38 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7157 (ptp90) REVERT: N 52 SER cc_start: 0.8602 (m) cc_final: 0.8242 (t) REVERT: N 120 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7356 (mt0) outliers start: 30 outliers final: 24 residues processed: 156 average time/residue: 1.1281 time to fit residues: 189.1653 Evaluate side-chains 164 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 266 VAL 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 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 78 LYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP 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 B residue 275 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.173533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.134689 restraints weight = 10769.255| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.80 r_work: 0.3673 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9019 Z= 0.153 Angle : 0.494 7.965 12196 Z= 0.260 Chirality : 0.041 0.273 1354 Planarity : 0.003 0.045 1517 Dihedral : 6.325 55.711 1597 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.80 % Allowed : 19.63 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1.15 (0.26), residues: 1050 helix: 3.08 (0.25), residues: 413 sheet: -0.14 (0.34), residues: 210 loop : -1.16 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE R 260 TYR 0.008 0.001 TYR R 363 ARG 0.010 0.000 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5921.76 seconds wall clock time: 105 minutes 21.46 seconds (6321.46 seconds total)