Starting phenix.real_space_refine on Sun Jul 27 03:26:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pb0_20284/07_2025/6pb0_20284.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pb0_20284/07_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_20284/07_2025/6pb0_20284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pb0_20284/07_2025/6pb0_20284.map" model { file = "/net/cci-nas-00/data/ceres_data/6pb0_20284/07_2025/6pb0_20284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pb0_20284/07_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-5711/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: 5.55, per 1000 atoms: 0.63 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: 2.36 Conformation dependent library (CDL) restraints added in 974.1 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: 1.02 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: 2.59 Time building geometry restraints manager: 2.77 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: 1.710 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.590 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: 0.010 Load rotamer database and sin/cos tables:16.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- 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 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 : 9.455 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 Details of bonding type rmsd hydrogen bonds : bond 0.14245 ( 440) hydrogen bonds : angle 6.00809 ( 1278) SS BOND : bond 0.00303 ( 3) SS BOND : angle 2.03465 ( 6) covalent geometry : bond 0.00363 ( 9019) covalent geometry : angle 0.82397 (12196) *********************** 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 : 0.948 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: 1.1100 time to fit residues: 305.9637 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 : 0.879 ------------------------------------------------------------------------------- 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 = 0.141560 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 9022 Z= 0.126 Angle : 0.503 5.333 12202 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 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 440) hydrogen bonds : angle 4.27871 ( 1278) SS BOND : bond 0.01140 ( 3) SS BOND : angle 1.14205 ( 6) covalent geometry : bond 0.00283 ( 9019) covalent geometry : angle 0.50205 (12196) *********************** 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 : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 292 ARG cc_start: 0.7508 (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: 0.7440 (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: 0.7791 (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: 0.6780 (t0) cc_final: 0.6518 (t0) REVERT: B 22 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7347 (ttm170) REVERT: B 189 SER cc_start: 0.8853 (p) cc_final: 0.8596 (m) REVERT: B 271 CYS cc_start: 0.8478 (m) cc_final: 0.7679 (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: 1.0640 time to fit residues: 219.4549 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 : 0.963 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 9.9990 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: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.170950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127303 restraints weight = 11158.086| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.05 r_work: 0.3576 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9022 Z= 0.291 Angle : 0.649 6.419 12202 Z= 0.342 Chirality : 0.046 0.157 1354 Planarity : 0.005 0.064 1517 Dihedral : 8.270 59.774 1597 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.07 % Allowed : 14.56 % Favored : 80.37 % 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: -0.32 (0.25), residues: 1050 helix: 1.56 (0.25), residues: 424 sheet: -1.05 (0.31), residues: 226 loop : -1.64 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 156 HIS 0.010 0.002 HIS A 220 PHE 0.022 0.002 PHE R 331 TYR 0.019 0.002 TYR N 94 ARG 0.010 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.05726 ( 440) hydrogen bonds : angle 4.57737 ( 1278) SS BOND : bond 0.00654 ( 3) SS BOND : angle 1.63301 ( 6) covalent geometry : bond 0.00699 ( 9019) covalent geometry : angle 0.64790 (12196) *********************** 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 209 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.839 Fit side-chains REVERT: R 377 ARG cc_start: 0.7367 (mtp85) cc_final: 0.6231 (tmt170) REVERT: U 8 ASP cc_start: 0.7392 (t70) cc_final: 0.7148 (t70) REVERT: A 222 PHE cc_start: 0.8142 (m-80) cc_final: 0.7901 (m-80) REVERT: A 230 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: A 284 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 343 ASP cc_start: 0.7788 (t0) cc_final: 0.7382 (t0) REVERT: B 42 ARG cc_start: 0.7849 (tpt90) cc_final: 0.7240 (ttt-90) REVERT: B 156 GLN cc_start: 0.8409 (mt0) cc_final: 0.7821 (mt0) REVERT: B 175 GLN cc_start: 0.7942 (mt0) cc_final: 0.7565 (mm-40) REVERT: B 234 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: B 254 ASP cc_start: 0.8414 (t70) cc_final: 0.8179 (t70) REVERT: B 258 ASP cc_start: 0.8224 (t70) cc_final: 0.7628 (t0) REVERT: B 271 CYS cc_start: 0.8662 (m) cc_final: 0.8019 (p) REVERT: G 40 TYR cc_start: 0.8648 (t80) cc_final: 0.8191 (t80) REVERT: N 120 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7446 (mt0) outliers start: 47 outliers final: 26 residues processed: 190 average time/residue: 1.0890 time to fit residues: 223.1298 Evaluate side-chains 168 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 135 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 256 GLU Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 328 MET Chi-restraints excluded: chain R residue 339 VAL Chi-restraints excluded: chain R residue 360 SER Chi-restraints excluded: chain R residue 361 VAL 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 B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET 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 G residue 38 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 49 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 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.0040 chunk 92 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 182 GLN A 264 ASN A 294 GLN B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.176652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133358 restraints weight = 10794.345| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.07 r_work: 0.3640 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9022 Z= 0.107 Angle : 0.485 7.253 12202 Z= 0.257 Chirality : 0.040 0.159 1354 Planarity : 0.004 0.038 1517 Dihedral : 7.148 59.996 1597 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.31 % Allowed : 17.48 % 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: 0.28 (0.26), residues: 1050 helix: 2.23 (0.25), residues: 422 sheet: -0.89 (0.32), residues: 218 loop : -1.41 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.001 PHE R 260 TYR 0.008 0.001 TYR R 363 ARG 0.007 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 440) hydrogen bonds : angle 4.00678 ( 1278) SS BOND : bond 0.00332 ( 3) SS BOND : angle 2.99073 ( 6) covalent geometry : bond 0.00239 ( 9019) covalent geometry : angle 0.48098 (12196) *********************** 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 185 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7328 (mtp85) cc_final: 0.6248 (tmt170) REVERT: A 222 PHE cc_start: 0.8177 (m-80) cc_final: 0.7840 (m-80) REVERT: A 284 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 343 ASP cc_start: 0.7631 (t0) cc_final: 0.7213 (t0) REVERT: B 42 ARG cc_start: 0.7912 (tpt90) cc_final: 0.7052 (ttt90) REVERT: B 156 GLN cc_start: 0.8199 (mt0) cc_final: 0.7651 (mt0) REVERT: B 175 GLN cc_start: 0.7958 (mt0) cc_final: 0.7511 (mm-40) REVERT: B 234 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: B 254 ASP cc_start: 0.8343 (t70) cc_final: 0.8115 (t70) REVERT: B 258 ASP cc_start: 0.7982 (t70) cc_final: 0.7375 (t0) REVERT: B 271 CYS cc_start: 0.8577 (m) cc_final: 0.7909 (p) REVERT: G 40 TYR cc_start: 0.8619 (t80) cc_final: 0.8235 (t80) REVERT: N 120 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7418 (mt0) outliers start: 40 outliers final: 18 residues processed: 166 average time/residue: 1.3287 time to fit residues: 236.8815 Evaluate side-chains 155 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 379 HIS Chi-restraints excluded: chain A residue 29 GLN 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 A residue 301 VAL 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 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 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: 2.9990 chunk 95 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.172564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129306 restraints weight = 10964.367| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.02 r_work: 0.3599 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9022 Z= 0.185 Angle : 0.547 7.348 12202 Z= 0.289 Chirality : 0.043 0.166 1354 Planarity : 0.004 0.041 1517 Dihedral : 7.431 59.641 1597 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.10 % Allowed : 17.04 % 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: 0.34 (0.26), residues: 1050 helix: 2.24 (0.25), residues: 421 sheet: -0.81 (0.32), residues: 222 loop : -1.33 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.002 PHE R 260 TYR 0.013 0.001 TYR A 339 ARG 0.009 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 440) hydrogen bonds : angle 4.18329 ( 1278) SS BOND : bond 0.00754 ( 3) SS BOND : angle 3.13018 ( 6) covalent geometry : bond 0.00441 ( 9019) covalent geometry : angle 0.54283 (12196) *********************** 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 178 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.879 Fit side-chains REVERT: R 182 GLN cc_start: 0.8319 (tp-100) cc_final: 0.7833 (tp-100) REVERT: R 377 ARG cc_start: 0.7351 (mtp85) cc_final: 0.6125 (tpt90) REVERT: U 8 ASP cc_start: 0.7194 (t70) cc_final: 0.6981 (t70) REVERT: A 217 VAL cc_start: 0.8438 (t) cc_final: 0.8188 (p) REVERT: A 222 PHE cc_start: 0.8208 (m-80) cc_final: 0.7932 (m-80) REVERT: A 230 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: A 284 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8445 (p) REVERT: A 343 ASP cc_start: 0.7692 (t0) cc_final: 0.7322 (t0) REVERT: B 42 ARG cc_start: 0.7934 (tpt90) cc_final: 0.7062 (ttt90) REVERT: B 175 GLN cc_start: 0.7904 (mt0) cc_final: 0.7458 (mm-40) REVERT: B 234 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: B 254 ASP cc_start: 0.8347 (t70) cc_final: 0.8114 (t70) REVERT: B 258 ASP cc_start: 0.8064 (t70) cc_final: 0.7483 (t0) REVERT: B 262 MET cc_start: 0.8329 (tpp) cc_final: 0.7298 (mmt) REVERT: B 271 CYS cc_start: 0.8656 (m) cc_final: 0.7993 (p) REVERT: G 40 TYR cc_start: 0.8665 (t80) cc_final: 0.8300 (t80) REVERT: N 38 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7133 (ptp90) REVERT: N 80 TYR cc_start: 0.6786 (m-80) cc_final: 0.6137 (m-80) REVERT: N 120 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7514 (mt0) outliers start: 38 outliers final: 23 residues processed: 162 average time/residue: 1.1521 time to fit residues: 199.5511 Evaluate side-chains 155 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 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 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 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: 2.9990 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.174533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131764 restraints weight = 10835.283| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.03 r_work: 0.3637 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9022 Z= 0.119 Angle : 0.484 5.886 12202 Z= 0.258 Chirality : 0.041 0.174 1354 Planarity : 0.004 0.043 1517 Dihedral : 6.944 59.034 1597 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.67 % Allowed : 18.34 % Favored : 77.99 % 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: 0.60 (0.26), residues: 1050 helix: 2.52 (0.25), residues: 419 sheet: -0.62 (0.32), residues: 220 loop : -1.30 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.009 0.001 TYR R 363 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 440) hydrogen bonds : angle 3.98888 ( 1278) SS BOND : bond 0.00257 ( 3) SS BOND : angle 2.57308 ( 6) covalent geometry : bond 0.00274 ( 9019) covalent geometry : angle 0.48069 (12196) *********************** 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 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: R 182 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7834 (tp-100) REVERT: R 377 ARG cc_start: 0.7356 (mtp85) cc_final: 0.6159 (tpt90) REVERT: A 217 VAL cc_start: 0.8428 (t) cc_final: 0.8161 (p) REVERT: A 265 ARG cc_start: 0.7421 (mmm160) cc_final: 0.7124 (mtp85) REVERT: A 284 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8468 (p) REVERT: A 343 ASP cc_start: 0.7651 (t0) cc_final: 0.7277 (t0) REVERT: B 42 ARG cc_start: 0.7938 (tpt90) cc_final: 0.7096 (ttt90) REVERT: B 59 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: B 175 GLN cc_start: 0.7912 (mt0) cc_final: 0.7470 (mm-40) REVERT: B 234 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: B 258 ASP cc_start: 0.8047 (t70) cc_final: 0.7474 (t0) REVERT: B 262 MET cc_start: 0.8264 (tpp) cc_final: 0.7259 (mmt) REVERT: B 271 CYS cc_start: 0.8603 (m) cc_final: 0.7983 (p) REVERT: G 40 TYR cc_start: 0.8673 (t80) cc_final: 0.8274 (t80) REVERT: N 38 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7208 (ptp90) REVERT: N 120 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7443 (mt0) outliers start: 34 outliers final: 24 residues processed: 159 average time/residue: 1.0674 time to fit residues: 182.5070 Evaluate side-chains 156 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 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 244 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 36 VAL 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 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 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: 6.9990 chunk 4 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 382 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.175149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.135157 restraints weight = 10725.158| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.88 r_work: 0.3666 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9022 Z= 0.099 Angle : 0.471 8.477 12202 Z= 0.250 Chirality : 0.040 0.178 1354 Planarity : 0.004 0.044 1517 Dihedral : 6.535 57.522 1597 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.13 % Allowed : 19.85 % Favored : 77.02 % 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: 0.84 (0.26), residues: 1050 helix: 2.83 (0.25), residues: 413 sheet: -0.57 (0.32), residues: 222 loop : -1.20 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.015 0.001 TYR N 60 ARG 0.012 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 440) hydrogen bonds : angle 3.84136 ( 1278) SS BOND : bond 0.00185 ( 3) SS BOND : angle 2.09964 ( 6) covalent geometry : bond 0.00218 ( 9019) covalent geometry : angle 0.46867 (12196) *********************** 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 172 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: R 182 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7981 (tm-30) REVERT: R 377 ARG cc_start: 0.7332 (mtp85) cc_final: 0.6261 (tmt170) REVERT: A 209 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 217 VAL cc_start: 0.8386 (t) cc_final: 0.8108 (p) REVERT: A 284 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 343 ASP cc_start: 0.7625 (t0) cc_final: 0.7235 (t0) REVERT: B 42 ARG cc_start: 0.7933 (tpt90) cc_final: 0.7092 (ttt90) REVERT: B 59 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 175 GLN cc_start: 0.7872 (mt0) cc_final: 0.7441 (mm-40) REVERT: B 234 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: B 239 ASN cc_start: 0.8298 (m-40) cc_final: 0.8042 (m110) REVERT: B 258 ASP cc_start: 0.7970 (t70) cc_final: 0.7435 (t0) REVERT: B 271 CYS cc_start: 0.8594 (m) cc_final: 0.7895 (p) REVERT: G 40 TYR cc_start: 0.8634 (t80) cc_final: 0.8314 (t80) REVERT: N 38 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7979 (ptt180) REVERT: N 120 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7377 (mt0) outliers start: 29 outliers final: 19 residues processed: 163 average time/residue: 1.1074 time to fit residues: 195.3553 Evaluate side-chains 156 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 339 VAL 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 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 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 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 79 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 0.0040 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.172246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133520 restraints weight = 10829.124| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.80 r_work: 0.3645 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9022 Z= 0.116 Angle : 0.492 7.263 12202 Z= 0.261 Chirality : 0.041 0.180 1354 Planarity : 0.004 0.044 1517 Dihedral : 6.512 57.086 1597 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.13 % Allowed : 20.60 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1050 helix: 2.90 (0.25), residues: 413 sheet: -0.50 (0.32), residues: 224 loop : -1.19 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.009 0.001 TYR R 363 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 440) hydrogen bonds : angle 3.87630 ( 1278) SS BOND : bond 0.00209 ( 3) SS BOND : angle 2.17097 ( 6) covalent geometry : bond 0.00266 ( 9019) covalent geometry : angle 0.48954 (12196) *********************** 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 165 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7351 (mtp85) cc_final: 0.6280 (tmt170) REVERT: A 217 VAL cc_start: 0.8381 (t) cc_final: 0.8117 (p) REVERT: A 230 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: A 265 ARG cc_start: 0.7361 (mmm160) cc_final: 0.7069 (mtp85) REVERT: A 284 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8479 (p) REVERT: A 343 ASP cc_start: 0.7675 (t0) cc_final: 0.7290 (t0) REVERT: B 42 ARG cc_start: 0.7948 (tpt90) cc_final: 0.7113 (ttt90) REVERT: B 59 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 175 GLN cc_start: 0.7872 (mt0) cc_final: 0.7458 (mm-40) REVERT: B 234 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: B 239 ASN cc_start: 0.8262 (m-40) cc_final: 0.7996 (m110) REVERT: B 258 ASP cc_start: 0.7950 (t70) cc_final: 0.7418 (t0) REVERT: B 262 MET cc_start: 0.8143 (tpp) cc_final: 0.7246 (mmt) REVERT: B 271 CYS cc_start: 0.8613 (m) cc_final: 0.7913 (p) REVERT: G 40 TYR cc_start: 0.8644 (t80) cc_final: 0.8243 (t80) REVERT: N 38 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7173 (ptp90) REVERT: N 120 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7373 (mt0) outliers start: 29 outliers final: 22 residues processed: 159 average time/residue: 1.0266 time to fit residues: 175.7683 Evaluate side-chains 157 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 78 LYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 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 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.174125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135550 restraints weight = 10747.128| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.78 r_work: 0.3668 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9022 Z= 0.101 Angle : 0.487 7.159 12202 Z= 0.258 Chirality : 0.040 0.198 1354 Planarity : 0.003 0.045 1517 Dihedral : 6.324 56.175 1597 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.13 % Allowed : 20.82 % Favored : 76.05 % 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: 0.99 (0.26), residues: 1050 helix: 3.00 (0.25), residues: 413 sheet: -0.45 (0.32), residues: 222 loop : -1.20 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.008 0.001 TYR R 363 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 440) hydrogen bonds : angle 3.79336 ( 1278) SS BOND : bond 0.00146 ( 3) SS BOND : angle 2.53239 ( 6) covalent geometry : bond 0.00228 ( 9019) covalent geometry : angle 0.48342 (12196) *********************** 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 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7349 (mtp85) cc_final: 0.6287 (tmt170) REVERT: A 217 VAL cc_start: 0.8353 (t) cc_final: 0.8124 (m) REVERT: A 230 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: A 284 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 343 ASP cc_start: 0.7665 (t0) cc_final: 0.7287 (t0) REVERT: B 42 ARG cc_start: 0.7911 (tpt90) cc_final: 0.7111 (ttt90) REVERT: B 59 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: B 175 GLN cc_start: 0.7848 (mt0) cc_final: 0.7438 (mm-40) REVERT: B 189 SER cc_start: 0.9007 (p) cc_final: 0.8545 (m) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: B 239 ASN cc_start: 0.8329 (m-40) cc_final: 0.8096 (m110) REVERT: B 258 ASP cc_start: 0.7965 (t70) cc_final: 0.7428 (t0) REVERT: B 271 CYS cc_start: 0.8616 (m) cc_final: 0.7909 (p) REVERT: G 40 TYR cc_start: 0.8623 (t80) cc_final: 0.8325 (t80) REVERT: N 38 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7983 (ptt180) REVERT: N 52 SER cc_start: 0.8578 (m) cc_final: 0.8237 (t) REVERT: N 120 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7271 (mt0) outliers start: 29 outliers final: 19 residues processed: 157 average time/residue: 1.0937 time to fit residues: 184.6219 Evaluate side-chains 154 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 78 LYS Chi-restraints excluded: chain B residue 96 ARG 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 N residue 38 ARG 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: 0.8980 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.172468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.133891 restraints weight = 10773.474| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.80 r_work: 0.3664 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4205 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= 0.117 Angle : 0.509 7.017 12202 Z= 0.268 Chirality : 0.041 0.241 1354 Planarity : 0.003 0.045 1517 Dihedral : 6.360 55.580 1597 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.80 % Allowed : 21.47 % Favored : 75.73 % 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: 1.05 (0.26), residues: 1050 helix: 3.01 (0.25), residues: 413 sheet: -0.36 (0.33), residues: 222 loop : -1.15 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.009 0.001 TYR R 363 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 440) hydrogen bonds : angle 3.85310 ( 1278) SS BOND : bond 0.00283 ( 3) SS BOND : angle 2.36260 ( 6) covalent geometry : bond 0.00271 ( 9019) covalent geometry : angle 0.50658 (12196) ********************** 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 162 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: R 377 ARG cc_start: 0.7354 (mtp85) cc_final: 0.6285 (tmt170) REVERT: A 217 VAL cc_start: 0.8368 (t) cc_final: 0.8095 (p) REVERT: A 230 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: A 265 ARG cc_start: 0.7337 (mmm160) cc_final: 0.7052 (mtp85) REVERT: A 284 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 343 ASP cc_start: 0.7668 (t0) cc_final: 0.7291 (t0) REVERT: B 42 ARG cc_start: 0.7952 (tpt90) cc_final: 0.7111 (ttt90) REVERT: B 59 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: B 175 GLN cc_start: 0.7822 (mt0) cc_final: 0.7411 (mm-40) REVERT: B 189 SER cc_start: 0.9029 (p) cc_final: 0.8583 (m) REVERT: B 198 LEU cc_start: 0.8820 (pt) cc_final: 0.8511 (mt) REVERT: B 234 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: B 239 ASN cc_start: 0.8273 (m-40) cc_final: 0.7983 (m110) REVERT: B 258 ASP cc_start: 0.7922 (t70) cc_final: 0.7383 (t0) REVERT: B 262 MET cc_start: 0.8067 (tpp) cc_final: 0.7170 (mmt) REVERT: B 271 CYS cc_start: 0.8625 (m) cc_final: 0.7913 (p) REVERT: G 40 TYR cc_start: 0.8621 (t80) cc_final: 0.8305 (t80) REVERT: N 38 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7208 (ptp90) REVERT: N 52 SER cc_start: 0.8665 (m) cc_final: 0.8331 (t) REVERT: N 120 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7212 (mt0) outliers start: 26 outliers final: 17 residues processed: 154 average time/residue: 1.0362 time to fit residues: 171.8709 Evaluate side-chains 153 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 78 LYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 38 ARG 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: 5.9990 chunk 97 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.173818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135006 restraints weight = 10752.736| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.79 r_work: 0.3670 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4206 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= 0.104 Angle : 0.499 7.980 12202 Z= 0.262 Chirality : 0.041 0.276 1354 Planarity : 0.003 0.045 1517 Dihedral : 6.214 54.783 1597 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.80 % Allowed : 21.68 % Favored : 75.51 % 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: 1.08 (0.26), residues: 1050 helix: 3.09 (0.25), residues: 413 sheet: -0.41 (0.33), residues: 222 loop : -1.16 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE A 222 TYR 0.009 0.001 TYR R 363 ARG 0.009 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 440) hydrogen bonds : angle 3.81148 ( 1278) SS BOND : bond 0.00252 ( 3) SS BOND : angle 2.08231 ( 6) covalent geometry : bond 0.00235 ( 9019) covalent geometry : angle 0.49723 (12196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6465.45 seconds wall clock time: 114 minutes 5.17 seconds (6845.17 seconds total)