Starting phenix.real_space_refine on Wed Aug 5 12:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9j_39081/08_2026/8y9j_39081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9j_39081/08_2026/8y9j_39081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9j_39081/08_2026/8y9j_39081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9j_39081/08_2026/8y9j_39081.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9j_39081/08_2026/8y9j_39081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9j_39081/08_2026/8y9j_39081.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 41 5.16 5 C 6190 2.51 5 N 1704 2.21 5 O 1823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9770 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3071 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 8, 'TRANS': 381} Chain: "B" Number of atoms: 3066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3066 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 8, 'TRANS': 380} Chain: "C" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1764 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain: "D" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1629 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain: "K" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 9} Time building chain proxies: 1.64, per 1000 atoms: 0.17 Number of scatterers: 9770 At special positions: 0 Unit cell: (116.325, 120.037, 106.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 12 15.00 O 1823 8.00 N 1704 7.00 C 6190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 328.2 milliseconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 69.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 48 through 64 removed outlier: 3.952A pdb=" N ILE A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 84 removed outlier: 3.808A pdb=" N GLN A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 91 removed outlier: 4.239A pdb=" N LEU A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 124 through 137 removed outlier: 4.138A pdb=" N ASN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.852A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 183 removed outlier: 4.021A pdb=" N LEU A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 221 removed outlier: 4.249A pdb=" N GLN A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.821A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 290 removed outlier: 3.714A pdb=" N GLU A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.648A pdb=" N ARG A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.665A pdb=" N ASN A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 329 Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.594A pdb=" N GLY A 333 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 366 removed outlier: 3.523A pdb=" N LEU A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 408 Processing helix chain 'B' and resid 21 through 28 removed outlier: 4.120A pdb=" N LEU B 25 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 64 removed outlier: 3.827A pdb=" N VAL B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 83 Processing helix chain 'B' and resid 85 through 93 removed outlier: 4.215A pdb=" N LEU B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.790A pdb=" N ASN B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 157 removed outlier: 4.017A pdb=" N PHE B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 removed outlier: 5.012A pdb=" N LYS B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 221 removed outlier: 3.610A pdb=" N ARG B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 240 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 270 through 291 removed outlier: 3.875A pdb=" N LYS B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Proline residue: B 295 - end of helix No H-bonds generated for 'chain 'B' and resid 292 through 297' Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.933A pdb=" N ASN B 307 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 329 removed outlier: 3.624A pdb=" N HIS B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.587A pdb=" N ASN B 335 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 367 removed outlier: 4.720A pdb=" N LEU B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 407 removed outlier: 3.756A pdb=" N GLU B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 27 removed outlier: 3.545A pdb=" N GLY C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.873A pdb=" N ALA C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.693A pdb=" N THR C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 81 Processing helix chain 'C' and resid 88 through 105 Processing helix chain 'C' and resid 115 through 130 removed outlier: 4.454A pdb=" N LEU C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 144 removed outlier: 3.900A pdb=" N GLN C 144 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 166 removed outlier: 3.567A pdb=" N SER C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.832A pdb=" N SER C 207 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 208 " --> pdb=" O ASP C 205 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN C 210 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 230 removed outlier: 3.758A pdb=" N LYS C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 61 removed outlier: 3.763A pdb=" N LYS D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 82 removed outlier: 3.798A pdb=" N ASN D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 75 " --> pdb=" O MET D 71 " (cutoff:3.500A) Proline residue: D 77 - end of helix Processing helix chain 'D' and resid 90 through 106 Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.852A pdb=" N ALA D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 144 Processing helix chain 'D' and resid 145 through 166 removed outlier: 4.085A pdb=" N MET D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 223 through 230 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44 removed outlier: 5.937A pdb=" N ARG A 39 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU A 107 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 41 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS A 109 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 43 " --> pdb=" O LYS A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 45 removed outlier: 6.435A pdb=" N ARG B 39 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU B 107 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 41 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LYS B 109 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 43 " --> pdb=" O LYS B 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 258 Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 87 removed outlier: 6.882A pdb=" N THR C 86 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N LEU C 221 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 179 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 33 Processing sheet with id=AA8, first strand: chain 'D' and resid 178 through 182 595 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2341 1.33 - 1.45: 2064 1.45 - 1.58: 5467 1.58 - 1.70: 23 1.70 - 1.82: 75 Bond restraints: 9970 Sorted by residual: bond pdb=" C4' U K 9 " pdb=" O4' U K 9 " ideal model delta sigma weight residual 1.454 1.406 0.048 1.00e-02 1.00e+04 2.35e+01 bond pdb=" C5' U K 12 " pdb=" C4' U K 12 " ideal model delta sigma weight residual 1.508 1.535 -0.027 7.00e-03 2.04e+04 1.54e+01 bond pdb=" N PRO D 77 " pdb=" CD PRO D 77 " ideal model delta sigma weight residual 1.473 1.419 0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" C4' U K 15 " pdb=" O4' U K 15 " ideal model delta sigma weight residual 1.454 1.417 0.037 1.00e-02 1.00e+04 1.40e+01 bond pdb=" N THR B 206 " pdb=" CA THR B 206 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.14e+01 ... (remaining 9965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 11000 2.57 - 5.13: 2276 5.13 - 7.70: 192 7.70 - 10.27: 36 10.27 - 12.83: 10 Bond angle restraints: 13514 Sorted by residual: angle pdb=" N VAL A 124 " pdb=" CA VAL A 124 " pdb=" C VAL A 124 " ideal model delta sigma weight residual 110.53 120.75 -10.22 9.40e-01 1.13e+00 1.18e+02 angle pdb=" C HIS B 290 " pdb=" N GLY B 291 " pdb=" CA GLY B 291 " ideal model delta sigma weight residual 120.13 132.96 -12.83 1.26e+00 6.30e-01 1.04e+02 angle pdb=" O4' U K 7 " pdb=" C1' U K 7 " pdb=" N1 U K 7 " ideal model delta sigma weight residual 108.50 115.46 -6.96 7.00e-01 2.04e+00 9.88e+01 angle pdb=" CA PHE B 66 " pdb=" CB PHE B 66 " pdb=" CG PHE B 66 " ideal model delta sigma weight residual 113.80 123.70 -9.90 1.00e+00 1.00e+00 9.81e+01 angle pdb=" CA PHE D 134 " pdb=" CB PHE D 134 " pdb=" CG PHE D 134 " ideal model delta sigma weight residual 113.80 122.88 -9.08 1.00e+00 1.00e+00 8.25e+01 ... (remaining 13509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.88: 5839 32.88 - 65.76: 198 65.76 - 98.64: 18 98.64 - 131.51: 0 131.51 - 164.39: 2 Dihedral angle restraints: 6057 sinusoidal: 2566 harmonic: 3491 Sorted by residual: dihedral pdb=" C5' U K 15 " pdb=" C4' U K 15 " pdb=" C3' U K 15 " pdb=" O3' U K 15 " ideal model delta sinusoidal sigma weight residual 147.00 67.57 79.43 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" O4' U K 15 " pdb=" C4' U K 15 " pdb=" C3' U K 15 " pdb=" C2' U K 15 " ideal model delta sinusoidal sigma weight residual 24.00 -38.37 62.37 1 8.00e+00 1.56e-02 8.04e+01 dihedral pdb=" C3' U K 15 " pdb=" C4' U K 15 " pdb=" O4' U K 15 " pdb=" C1' U K 15 " ideal model delta sinusoidal sigma weight residual -2.00 49.77 -51.77 1 8.00e+00 1.56e-02 5.72e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 1317 0.156 - 0.311: 212 0.311 - 0.467: 27 0.467 - 0.622: 4 0.622 - 0.778: 3 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CA ASN A 301 " pdb=" N ASN A 301 " pdb=" C ASN A 301 " pdb=" CB ASN A 301 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CA ASN A 306 " pdb=" N ASN A 306 " pdb=" C ASN A 306 " pdb=" CB ASN A 306 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ILE B 254 " pdb=" N ILE B 254 " pdb=" C ILE B 254 " pdb=" CB ILE B 254 " both_signs ideal model delta sigma weight residual False 2.43 1.79 0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 1560 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U K 16 " 0.376 2.00e-02 2.50e+03 1.74e-01 6.80e+02 pdb=" N1 U K 16 " -0.109 2.00e-02 2.50e+03 pdb=" C2 U K 16 " -0.119 2.00e-02 2.50e+03 pdb=" O2 U K 16 " -0.107 2.00e-02 2.50e+03 pdb=" N3 U K 16 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U K 16 " 0.054 2.00e-02 2.50e+03 pdb=" O4 U K 16 " 0.203 2.00e-02 2.50e+03 pdb=" C5 U K 16 " -0.106 2.00e-02 2.50e+03 pdb=" C6 U K 16 " -0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U K 11 " -0.246 2.00e-02 2.50e+03 1.23e-01 3.43e+02 pdb=" N1 U K 11 " 0.039 2.00e-02 2.50e+03 pdb=" C2 U K 11 " 0.008 2.00e-02 2.50e+03 pdb=" O2 U K 11 " 0.152 2.00e-02 2.50e+03 pdb=" N3 U K 11 " -0.039 2.00e-02 2.50e+03 pdb=" C4 U K 11 " -0.028 2.00e-02 2.50e+03 pdb=" O4 U K 11 " -0.135 2.00e-02 2.50e+03 pdb=" C5 U K 11 " 0.109 2.00e-02 2.50e+03 pdb=" C6 U K 11 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U K 15 " 0.207 2.00e-02 2.50e+03 1.20e-01 3.27e+02 pdb=" N1 U K 15 " 0.020 2.00e-02 2.50e+03 pdb=" C2 U K 15 " 0.009 2.00e-02 2.50e+03 pdb=" O2 U K 15 " -0.183 2.00e-02 2.50e+03 pdb=" N3 U K 15 " 0.068 2.00e-02 2.50e+03 pdb=" C4 U K 15 " 0.023 2.00e-02 2.50e+03 pdb=" O4 U K 15 " 0.119 2.00e-02 2.50e+03 pdb=" C5 U K 15 " -0.132 2.00e-02 2.50e+03 pdb=" C6 U K 15 " -0.130 2.00e-02 2.50e+03 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3262 2.88 - 3.39: 11057 3.39 - 3.89: 16423 3.89 - 4.40: 18673 4.40 - 4.90: 29426 Nonbonded interactions: 78841 Sorted by model distance: nonbonded pdb=" O ALA A 403 " pdb=" OG1 THR A 406 " model vdw 2.376 3.040 nonbonded pdb=" O ALA B 403 " pdb=" OG1 THR B 406 " model vdw 2.452 3.040 nonbonded pdb=" O ILE A 215 " pdb=" N GLY A 218 " model vdw 2.503 3.120 nonbonded pdb=" O3' U K 9 " pdb=" O2' U K 9 " model vdw 2.511 2.432 nonbonded pdb=" O2' U K 15 " pdb=" OP1 U K 16 " model vdw 2.561 3.040 ... (remaining 78836 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 407) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 28 through 231) selection = chain 'D' } 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 group one per residue 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: 1.130 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.500 Find NCS groups from input model: 0.190 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.012 0.054 9970 Z= 0.780 Angle : 2.024 12.832 13514 Z= 1.428 Chirality : 0.121 0.778 1563 Planarity : 0.021 0.391 1689 Dihedral : 16.841 164.392 3789 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 2.01 % Allowed : 7.35 % Favored : 90.64 % Rotamer: Outliers : 2.23 % Allowed : 7.47 % Favored : 90.30 % Cbeta Deviations : 1.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.20), residues: 1197 helix: -1.13 (0.16), residues: 663 sheet: 0.89 (0.50), residues: 88 loop : -2.94 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 361 TYR 0.208 0.032 TYR B 340 PHE 0.162 0.021 PHE D 134 TRP 0.142 0.026 TRP C 42 HIS 0.016 0.004 HIS D 58 Details of bonding type rmsd/Z covalent geometry : bond 0.01227 / 0.78 ( 9970) covalent geometry : angle 2.02434 / 1.43 (13514) hydrogen bonds : bond 0.18979 / 13.04 ( 595) hydrogen bonds : angle 8.88888 / 6.48 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 443 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9007 (mt) cc_final: 0.8480 (mt) REVERT: A 98 TYR cc_start: 0.7481 (t80) cc_final: 0.7258 (t80) REVERT: A 105 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8581 (ttt-90) REVERT: A 107 GLU cc_start: 0.8975 (pt0) cc_final: 0.8737 (pt0) REVERT: A 110 LYS cc_start: 0.9692 (tptm) cc_final: 0.9303 (tppp) REVERT: A 128 LYS cc_start: 0.8983 (pttt) cc_final: 0.8778 (pttm) REVERT: A 174 ARG cc_start: 0.9297 (mtt180) cc_final: 0.9091 (mtp85) REVERT: A 179 HIS cc_start: 0.8726 (m-70) cc_final: 0.8508 (m-70) REVERT: A 199 VAL cc_start: 0.9194 (t) cc_final: 0.8958 (m) REVERT: A 204 MET cc_start: 0.8595 (mmt) cc_final: 0.8015 (tpp) REVERT: A 211 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8179 (mtmt) REVERT: A 253 HIS cc_start: 0.8442 (m90) cc_final: 0.8155 (m90) REVERT: A 280 PHE cc_start: 0.9574 (t80) cc_final: 0.8795 (t80) REVERT: A 327 HIS cc_start: 0.7234 (m170) cc_final: 0.6577 (m-70) REVERT: A 342 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.9046 (mp10) REVERT: A 371 GLN cc_start: 0.9504 (mm-40) cc_final: 0.9262 (mp10) REVERT: A 372 GLU cc_start: 0.9503 (mp0) cc_final: 0.9236 (mp0) REVERT: A 376 LEU cc_start: 0.9803 (mm) cc_final: 0.9475 (mm) REVERT: A 380 HIS cc_start: 0.9494 (m-70) cc_final: 0.9174 (m-70) REVERT: A 398 ARG cc_start: 0.9073 (ptt90) cc_final: 0.8773 (ttp-110) REVERT: B 19 MET cc_start: 0.6513 (pmm) cc_final: 0.5582 (pmm) REVERT: B 157 PHE cc_start: 0.9471 (m-80) cc_final: 0.9122 (m-80) REVERT: B 194 VAL cc_start: 0.8833 (t) cc_final: 0.8556 (t) REVERT: B 196 HIS cc_start: 0.9203 (m-70) cc_final: 0.8584 (m-70) REVERT: B 198 MET cc_start: 0.8960 (mmm) cc_final: 0.8442 (mmm) REVERT: B 221 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7869 (ppp) REVERT: B 222 VAL cc_start: 0.5646 (OUTLIER) cc_final: 0.5103 (t) REVERT: B 234 ASN cc_start: 0.9370 (t0) cc_final: 0.9149 (t0) REVERT: B 327 HIS cc_start: 0.8087 (m-70) cc_final: 0.7873 (m90) REVERT: B 330 THR cc_start: 0.9374 (p) cc_final: 0.9032 (t) REVERT: B 344 ARG cc_start: 0.9031 (ttt-90) cc_final: 0.8638 (tpt-90) REVERT: B 354 LEU cc_start: 0.9646 (mt) cc_final: 0.9431 (mm) REVERT: B 355 GLN cc_start: 0.9212 (mt0) cc_final: 0.8647 (mp10) REVERT: B 363 LEU cc_start: 0.9389 (mt) cc_final: 0.9106 (mt) REVERT: B 374 LYS cc_start: 0.9309 (mtmm) cc_final: 0.8964 (mttp) REVERT: B 376 LEU cc_start: 0.9718 (mt) cc_final: 0.9465 (mt) REVERT: B 380 HIS cc_start: 0.9442 (m90) cc_final: 0.9008 (m90) REVERT: B 384 ASN cc_start: 0.9073 (m-40) cc_final: 0.8858 (m110) REVERT: C 52 LYS cc_start: 0.6452 (mttm) cc_final: 0.6105 (mmmt) REVERT: C 80 PHE cc_start: 0.8714 (t80) cc_final: 0.8489 (t80) REVERT: C 136 MET cc_start: -0.3641 (tmm) cc_final: -0.4004 (mmm) REVERT: C 159 LYS cc_start: 0.8174 (mttt) cc_final: 0.7837 (tptp) REVERT: C 160 PHE cc_start: 0.8835 (t80) cc_final: 0.8338 (t80) REVERT: C 186 HIS cc_start: 0.8755 (m90) cc_final: 0.8478 (m170) REVERT: C 191 THR cc_start: 0.8918 (m) cc_final: 0.8692 (p) REVERT: C 195 MET cc_start: 0.0881 (ttm) cc_final: 0.0547 (ttp) REVERT: C 200 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7762 (mt-10) REVERT: C 213 LYS cc_start: 0.8815 (tttt) cc_final: 0.8479 (tmtt) REVERT: C 230 PHE cc_start: 0.6001 (t80) cc_final: 0.5793 (t80) REVERT: D 30 LEU cc_start: 0.8749 (mt) cc_final: 0.8142 (mt) REVERT: D 92 TRP cc_start: 0.8405 (p-90) cc_final: 0.8051 (p-90) REVERT: D 121 LEU cc_start: 0.9313 (mt) cc_final: 0.8978 (mt) REVERT: D 124 ASP cc_start: 0.9678 (m-30) cc_final: 0.9473 (p0) REVERT: D 157 ILE cc_start: 0.9257 (mt) cc_final: 0.8975 (mt) REVERT: D 165 ASP cc_start: 0.9229 (m-30) cc_final: 0.8932 (m-30) REVERT: D 209 MET cc_start: 0.2058 (ppp) cc_final: 0.0305 (mmm) outliers start: 23 outliers final: 9 residues processed: 458 average time/residue: 0.1030 time to fit residues: 65.0436 Evaluate side-chains 339 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 327 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 175 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 228 ASN B 306 ASN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** C 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS D 202 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.122121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097645 restraints weight = 31612.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100841 restraints weight = 21270.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.103225 restraints weight = 15659.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.105074 restraints weight = 12202.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.106433 restraints weight = 9928.137| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9970 Z= 0.246 Angle : 0.988 13.713 13514 Z= 0.535 Chirality : 0.052 0.331 1563 Planarity : 0.008 0.167 1689 Dihedral : 13.079 139.830 1464 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.52 % Favored : 89.89 % Rotamer: Outliers : 0.39 % Allowed : 4.36 % Favored : 95.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 1.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.22), residues: 1197 helix: -0.23 (0.18), residues: 678 sheet: 0.57 (0.45), residues: 112 loop : -2.78 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 192 TYR 0.045 0.004 TYR A 44 PHE 0.036 0.003 PHE A 296 TRP 0.034 0.003 TRP C 92 HIS 0.009 0.002 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.25 ( 9970) covalent geometry : angle 0.98761 / 0.53 (13514) hydrogen bonds : bond 0.07549 / 5.24 ( 595) hydrogen bonds : angle 6.91523 / 5.07 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 361 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.9009 (tmm) cc_final: 0.8537 (tmm) REVERT: A 77 LEU cc_start: 0.9205 (mt) cc_final: 0.8582 (mt) REVERT: A 98 TYR cc_start: 0.7524 (t80) cc_final: 0.7299 (t80) REVERT: A 110 LYS cc_start: 0.9310 (tptm) cc_final: 0.8927 (tppp) REVERT: A 153 PHE cc_start: 0.9156 (t80) cc_final: 0.8664 (t80) REVERT: A 174 ARG cc_start: 0.9345 (mtt180) cc_final: 0.9121 (mtp180) REVERT: A 179 HIS cc_start: 0.8506 (m-70) cc_final: 0.8123 (m-70) REVERT: A 213 LEU cc_start: 0.9482 (tt) cc_final: 0.9150 (tt) REVERT: A 372 GLU cc_start: 0.9487 (mp0) cc_final: 0.9155 (mp0) REVERT: A 376 LEU cc_start: 0.9745 (mm) cc_final: 0.9281 (mm) REVERT: A 380 HIS cc_start: 0.9387 (m-70) cc_final: 0.8836 (m90) REVERT: B 19 MET cc_start: 0.7814 (pmm) cc_final: 0.7092 (pmm) REVERT: B 76 MET cc_start: 0.9384 (ptp) cc_final: 0.9024 (ptt) REVERT: B 78 CYS cc_start: 0.8592 (p) cc_final: 0.8346 (p) REVERT: B 162 VAL cc_start: 0.8856 (t) cc_final: 0.8634 (t) REVERT: B 179 HIS cc_start: 0.8721 (m-70) cc_final: 0.8435 (m-70) REVERT: B 284 LEU cc_start: 0.9592 (mm) cc_final: 0.9082 (pp) REVERT: B 376 LEU cc_start: 0.9712 (mt) cc_final: 0.9307 (mt) REVERT: B 377 MET cc_start: 0.9237 (tmm) cc_final: 0.8637 (tmm) REVERT: B 380 HIS cc_start: 0.9306 (m90) cc_final: 0.8786 (m90) REVERT: B 381 GLN cc_start: 0.9557 (tt0) cc_final: 0.8943 (pt0) REVERT: B 382 LYS cc_start: 0.9588 (mtmm) cc_final: 0.9355 (mtmm) REVERT: C 42 TRP cc_start: 0.8523 (t60) cc_final: 0.7864 (t60) REVERT: C 159 LYS cc_start: 0.8254 (mttt) cc_final: 0.7865 (tptp) REVERT: C 160 PHE cc_start: 0.8899 (t80) cc_final: 0.8596 (t80) REVERT: C 181 ILE cc_start: 0.8553 (mm) cc_final: 0.7696 (mp) REVERT: C 191 THR cc_start: 0.9288 (m) cc_final: 0.9084 (p) REVERT: C 198 LEU cc_start: 0.9202 (tp) cc_final: 0.8955 (tp) REVERT: C 200 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8765 (mt-10) REVERT: C 213 LYS cc_start: 0.8891 (tttt) cc_final: 0.8511 (tmtt) REVERT: C 222 LEU cc_start: 0.9433 (pp) cc_final: 0.9138 (tp) REVERT: D 35 ILE cc_start: 0.8930 (tp) cc_final: 0.8678 (tp) REVERT: D 109 GLN cc_start: 0.8774 (mt0) cc_final: 0.8438 (tt0) REVERT: D 115 LEU cc_start: 0.9367 (mt) cc_final: 0.8708 (tt) REVERT: D 119 LEU cc_start: 0.9683 (mt) cc_final: 0.9448 (mt) REVERT: D 121 LEU cc_start: 0.9184 (mt) cc_final: 0.8861 (mt) REVERT: D 124 ASP cc_start: 0.9574 (m-30) cc_final: 0.9056 (p0) REVERT: D 149 MET cc_start: 0.9388 (mpp) cc_final: 0.9106 (mpp) outliers start: 4 outliers final: 0 residues processed: 362 average time/residue: 0.1029 time to fit residues: 51.5719 Evaluate side-chains 298 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN A 196 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.100423 restraints weight = 30971.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.103865 restraints weight = 20712.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.106478 restraints weight = 15063.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108423 restraints weight = 11594.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.109887 restraints weight = 9347.497| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9970 Z= 0.198 Angle : 0.876 16.429 13514 Z= 0.473 Chirality : 0.048 0.242 1563 Planarity : 0.007 0.162 1689 Dihedral : 11.991 138.802 1464 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.69 % Favored : 89.89 % Rotamer: Outliers : 0.19 % Allowed : 4.46 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.23), residues: 1197 helix: -0.01 (0.19), residues: 683 sheet: 0.70 (0.46), residues: 109 loop : -2.69 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 298 TYR 0.020 0.003 TYR B 98 PHE 0.042 0.003 PHE B 66 TRP 0.019 0.002 TRP D 69 HIS 0.033 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 ( 9970) covalent geometry : angle 0.87617 / 0.47 (13514) hydrogen bonds : bond 0.06757 / 4.69 ( 595) hydrogen bonds : angle 6.54790 / 4.76 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8432 (pmm) cc_final: 0.8172 (pmm) REVERT: A 76 MET cc_start: 0.9031 (tmm) cc_final: 0.8555 (tmm) REVERT: A 77 LEU cc_start: 0.9195 (mt) cc_final: 0.8498 (mt) REVERT: A 79 LEU cc_start: 0.9100 (mm) cc_final: 0.8791 (mm) REVERT: A 116 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7661 (mmp80) REVERT: A 132 ARG cc_start: 0.8725 (mtm110) cc_final: 0.8298 (mtm180) REVERT: A 153 PHE cc_start: 0.9035 (t80) cc_final: 0.8829 (t80) REVERT: A 174 ARG cc_start: 0.9313 (mtt180) cc_final: 0.9087 (mtp180) REVERT: A 179 HIS cc_start: 0.8523 (m-70) cc_final: 0.8091 (m-70) REVERT: A 211 LYS cc_start: 0.9418 (mttt) cc_final: 0.9155 (mttp) REVERT: A 308 LEU cc_start: 0.8456 (mm) cc_final: 0.7914 (mm) REVERT: A 309 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8055 (mt-10) REVERT: A 313 PHE cc_start: 0.8848 (m-10) cc_final: 0.8269 (m-10) REVERT: A 376 LEU cc_start: 0.9677 (mm) cc_final: 0.9317 (mm) REVERT: A 377 MET cc_start: 0.9163 (tmm) cc_final: 0.8756 (tmm) REVERT: A 379 PHE cc_start: 0.9483 (t80) cc_final: 0.9199 (t80) REVERT: A 380 HIS cc_start: 0.9274 (m-70) cc_final: 0.8621 (m-70) REVERT: B 21 TYR cc_start: 0.7501 (m-80) cc_final: 0.7047 (m-80) REVERT: B 74 LEU cc_start: 0.9435 (mt) cc_final: 0.9230 (mt) REVERT: B 76 MET cc_start: 0.9317 (ptp) cc_final: 0.9057 (ptt) REVERT: B 78 CYS cc_start: 0.8630 (p) cc_final: 0.8384 (p) REVERT: B 162 VAL cc_start: 0.8702 (t) cc_final: 0.8491 (t) REVERT: B 196 HIS cc_start: 0.8389 (m-70) cc_final: 0.8062 (m-70) REVERT: B 221 MET cc_start: 0.7512 (ptm) cc_final: 0.7285 (ppp) REVERT: B 284 LEU cc_start: 0.9520 (mm) cc_final: 0.9059 (pp) REVERT: B 338 GLU cc_start: 0.8072 (pm20) cc_final: 0.7695 (pm20) REVERT: B 363 LEU cc_start: 0.9353 (mt) cc_final: 0.9123 (mt) REVERT: B 376 LEU cc_start: 0.9689 (mt) cc_final: 0.9302 (mt) REVERT: C 76 PHE cc_start: 0.9030 (m-80) cc_final: 0.8772 (m-80) REVERT: C 159 LYS cc_start: 0.8085 (mttt) cc_final: 0.7726 (tptp) REVERT: C 160 PHE cc_start: 0.8798 (t80) cc_final: 0.8523 (t80) REVERT: C 191 THR cc_start: 0.9121 (m) cc_final: 0.8563 (p) REVERT: C 198 LEU cc_start: 0.9179 (tp) cc_final: 0.8897 (tp) REVERT: C 200 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 213 LYS cc_start: 0.8887 (tttt) cc_final: 0.8503 (tmtt) REVERT: C 222 LEU cc_start: 0.9385 (pp) cc_final: 0.9101 (tt) REVERT: D 115 LEU cc_start: 0.9332 (mt) cc_final: 0.8751 (tt) REVERT: D 119 LEU cc_start: 0.9682 (mt) cc_final: 0.9462 (mt) REVERT: D 121 LEU cc_start: 0.9107 (mt) cc_final: 0.8702 (mt) REVERT: D 124 ASP cc_start: 0.9558 (m-30) cc_final: 0.8945 (p0) REVERT: D 149 MET cc_start: 0.9297 (mpp) cc_final: 0.8722 (mpp) REVERT: D 165 ASP cc_start: 0.9247 (m-30) cc_final: 0.8966 (m-30) REVERT: D 219 PHE cc_start: 0.6568 (p90) cc_final: 0.6332 (p90) outliers start: 2 outliers final: 0 residues processed: 349 average time/residue: 0.1014 time to fit residues: 49.2685 Evaluate side-chains 297 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 109 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN D 186 HIS ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.124759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100054 restraints weight = 31822.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103401 restraints weight = 21462.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.105942 restraints weight = 15703.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.107814 restraints weight = 12132.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.109258 restraints weight = 9831.795| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9970 Z= 0.186 Angle : 0.830 12.599 13514 Z= 0.448 Chirality : 0.047 0.247 1563 Planarity : 0.007 0.157 1689 Dihedral : 11.344 135.529 1464 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.19 % Favored : 90.39 % Rotamer: Outliers : 0.19 % Allowed : 3.98 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1197 helix: -0.02 (0.19), residues: 677 sheet: 0.92 (0.46), residues: 112 loop : -2.60 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 398 TYR 0.024 0.002 TYR B 98 PHE 0.031 0.003 PHE B 66 TRP 0.046 0.002 TRP D 92 HIS 0.021 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 ( 9970) covalent geometry : angle 0.82960 / 0.45 (13514) hydrogen bonds : bond 0.06295 / 4.37 ( 595) hydrogen bonds : angle 6.37364 / 4.66 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 351 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9032 (mm) cc_final: 0.8787 (mm) REVERT: A 110 LYS cc_start: 0.9017 (tptt) cc_final: 0.8779 (tppp) REVERT: A 116 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.8003 (mmt-90) REVERT: A 132 ARG cc_start: 0.8724 (mtm110) cc_final: 0.8478 (mtm180) REVERT: A 153 PHE cc_start: 0.9185 (t80) cc_final: 0.8836 (t80) REVERT: A 174 ARG cc_start: 0.9331 (mtt180) cc_final: 0.9121 (mtp180) REVERT: A 179 HIS cc_start: 0.8542 (m-70) cc_final: 0.8118 (m-70) REVERT: A 204 MET cc_start: 0.8406 (tpp) cc_final: 0.7744 (tpp) REVERT: A 211 LYS cc_start: 0.9309 (mttt) cc_final: 0.8815 (mttt) REVERT: A 376 LEU cc_start: 0.9665 (mm) cc_final: 0.9346 (mm) REVERT: A 379 PHE cc_start: 0.9406 (t80) cc_final: 0.9173 (t80) REVERT: A 380 HIS cc_start: 0.9242 (m-70) cc_final: 0.8624 (m-70) REVERT: A 390 GLN cc_start: 0.9635 (mm110) cc_final: 0.9298 (mt0) REVERT: B 21 TYR cc_start: 0.7552 (m-80) cc_final: 0.6892 (m-80) REVERT: B 29 LEU cc_start: 0.9081 (tp) cc_final: 0.8791 (tp) REVERT: B 57 ILE cc_start: 0.9170 (tt) cc_final: 0.8407 (tt) REVERT: B 74 LEU cc_start: 0.9403 (mt) cc_final: 0.9197 (mt) REVERT: B 78 CYS cc_start: 0.8636 (p) cc_final: 0.8404 (p) REVERT: B 179 HIS cc_start: 0.8793 (m-70) cc_final: 0.8357 (m-70) REVERT: B 192 GLN cc_start: 0.7407 (mt0) cc_final: 0.6983 (mp10) REVERT: B 196 HIS cc_start: 0.8129 (m-70) cc_final: 0.7851 (m-70) REVERT: B 327 HIS cc_start: 0.8794 (m170) cc_final: 0.8557 (m170) REVERT: B 344 ARG cc_start: 0.9188 (ttt-90) cc_final: 0.8457 (mtp180) REVERT: B 354 LEU cc_start: 0.9587 (mm) cc_final: 0.9381 (mm) REVERT: B 363 LEU cc_start: 0.9381 (mt) cc_final: 0.8996 (mt) REVERT: B 376 LEU cc_start: 0.9683 (mt) cc_final: 0.9294 (mt) REVERT: B 377 MET cc_start: 0.9555 (ttm) cc_final: 0.9157 (mtp) REVERT: B 380 HIS cc_start: 0.9129 (m90) cc_final: 0.8763 (m90) REVERT: C 159 LYS cc_start: 0.7919 (mttt) cc_final: 0.7645 (tptp) REVERT: C 160 PHE cc_start: 0.8743 (t80) cc_final: 0.8475 (t80) REVERT: C 191 THR cc_start: 0.9104 (m) cc_final: 0.8670 (p) REVERT: C 198 LEU cc_start: 0.9224 (tp) cc_final: 0.8873 (tp) REVERT: C 200 GLU cc_start: 0.8670 (mt-10) cc_final: 0.7929 (mt-10) REVERT: C 213 LYS cc_start: 0.8872 (tttt) cc_final: 0.8492 (tmtt) REVERT: C 222 LEU cc_start: 0.9380 (pp) cc_final: 0.9095 (tp) REVERT: D 35 ILE cc_start: 0.8715 (tp) cc_final: 0.8498 (mp) REVERT: D 115 LEU cc_start: 0.9258 (mt) cc_final: 0.8727 (tt) REVERT: D 124 ASP cc_start: 0.9595 (m-30) cc_final: 0.9351 (m-30) REVERT: D 126 LEU cc_start: 0.9791 (mt) cc_final: 0.9577 (mt) REVERT: D 149 MET cc_start: 0.9175 (mpp) cc_final: 0.8669 (mpp) REVERT: D 167 LEU cc_start: 0.6480 (mm) cc_final: 0.5605 (pt) REVERT: D 181 ILE cc_start: 0.7013 (mm) cc_final: 0.6787 (mm) REVERT: D 187 THR cc_start: 0.8438 (m) cc_final: 0.8051 (p) outliers start: 2 outliers final: 0 residues processed: 351 average time/residue: 0.1002 time to fit residues: 49.4957 Evaluate side-chains 295 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN D 33 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.123388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098425 restraints weight = 32394.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101675 restraints weight = 22285.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104087 restraints weight = 16568.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.105965 restraints weight = 13030.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.107294 restraints weight = 10676.815| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9970 Z= 0.196 Angle : 0.841 11.679 13514 Z= 0.454 Chirality : 0.046 0.252 1563 Planarity : 0.007 0.160 1689 Dihedral : 11.242 130.796 1464 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.86 % Favored : 89.72 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.23), residues: 1197 helix: -0.14 (0.19), residues: 690 sheet: 0.80 (0.47), residues: 112 loop : -2.56 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 298 TYR 0.026 0.002 TYR B 98 PHE 0.032 0.003 PHE A 201 TRP 0.026 0.003 TRP D 92 HIS 0.015 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 ( 9970) covalent geometry : angle 0.84083 / 0.45 (13514) hydrogen bonds : bond 0.06129 / 4.25 ( 595) hydrogen bonds : angle 6.32025 / 4.59 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8498 (pmm) cc_final: 0.8268 (pmm) REVERT: A 76 MET cc_start: 0.9066 (ptp) cc_final: 0.8808 (ppp) REVERT: A 77 LEU cc_start: 0.9201 (mt) cc_final: 0.8565 (mt) REVERT: A 79 LEU cc_start: 0.9062 (mm) cc_final: 0.8817 (mm) REVERT: A 116 ARG cc_start: 0.8313 (mmt-90) cc_final: 0.8001 (mmt-90) REVERT: A 132 ARG cc_start: 0.8767 (mtm110) cc_final: 0.8501 (mtm180) REVERT: A 153 PHE cc_start: 0.9212 (t80) cc_final: 0.8800 (t80) REVERT: A 174 ARG cc_start: 0.9363 (mtt180) cc_final: 0.9082 (mtp180) REVERT: A 179 HIS cc_start: 0.8437 (m-70) cc_final: 0.8036 (m-70) REVERT: A 204 MET cc_start: 0.8462 (tpp) cc_final: 0.7815 (tpp) REVERT: A 211 LYS cc_start: 0.9216 (mttt) cc_final: 0.8677 (mttt) REVERT: A 377 MET cc_start: 0.9204 (tmm) cc_final: 0.8865 (tmm) REVERT: B 54 GLN cc_start: 0.9540 (pp30) cc_final: 0.9164 (pp30) REVERT: B 55 LEU cc_start: 0.9183 (mt) cc_final: 0.8785 (mt) REVERT: B 74 LEU cc_start: 0.9414 (mt) cc_final: 0.9183 (mt) REVERT: B 78 CYS cc_start: 0.8730 (p) cc_final: 0.8497 (p) REVERT: B 100 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8634 (tp30) REVERT: B 192 GLN cc_start: 0.7397 (mt0) cc_final: 0.6987 (mp10) REVERT: B 307 ASN cc_start: 0.8193 (m110) cc_final: 0.7606 (t0) REVERT: B 340 TYR cc_start: 0.8981 (m-80) cc_final: 0.8644 (m-80) REVERT: B 344 ARG cc_start: 0.9238 (ttt-90) cc_final: 0.8661 (mtp180) REVERT: B 363 LEU cc_start: 0.9385 (mt) cc_final: 0.8940 (mt) REVERT: B 376 LEU cc_start: 0.9692 (mt) cc_final: 0.9233 (mt) REVERT: B 377 MET cc_start: 0.9604 (ttm) cc_final: 0.9241 (mtp) REVERT: B 380 HIS cc_start: 0.9105 (m90) cc_final: 0.8568 (m90) REVERT: C 58 HIS cc_start: 0.9236 (m170) cc_final: 0.8975 (m170) REVERT: C 76 PHE cc_start: 0.9137 (m-80) cc_final: 0.8861 (m-80) REVERT: C 149 MET cc_start: 0.6467 (ptp) cc_final: 0.6265 (ptt) REVERT: C 159 LYS cc_start: 0.7935 (mttt) cc_final: 0.7702 (tptp) REVERT: C 160 PHE cc_start: 0.8715 (t80) cc_final: 0.8447 (t80) REVERT: C 189 ILE cc_start: 0.7900 (mt) cc_final: 0.7697 (mm) REVERT: C 191 THR cc_start: 0.9170 (m) cc_final: 0.8519 (p) REVERT: C 200 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8368 (mt-10) REVERT: C 213 LYS cc_start: 0.8910 (tttt) cc_final: 0.8582 (tmtt) REVERT: C 222 LEU cc_start: 0.9276 (pp) cc_final: 0.8974 (tt) REVERT: D 31 VAL cc_start: 0.9145 (p) cc_final: 0.8664 (p) REVERT: D 35 ILE cc_start: 0.8639 (tp) cc_final: 0.8304 (mp) REVERT: D 109 GLN cc_start: 0.7898 (tt0) cc_final: 0.7558 (tp-100) REVERT: D 115 LEU cc_start: 0.9281 (mt) cc_final: 0.8694 (tt) REVERT: D 124 ASP cc_start: 0.9635 (m-30) cc_final: 0.9371 (m-30) REVERT: D 149 MET cc_start: 0.9069 (mpp) cc_final: 0.8381 (mpp) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1013 time to fit residues: 47.2118 Evaluate side-chains 279 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.124301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.099647 restraints weight = 31590.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.102802 restraints weight = 21476.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105281 restraints weight = 15905.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.107153 restraints weight = 12406.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.108459 restraints weight = 10070.968| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9970 Z= 0.185 Angle : 0.828 12.175 13514 Z= 0.446 Chirality : 0.046 0.254 1563 Planarity : 0.007 0.157 1689 Dihedral : 11.064 130.426 1464 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.86 % Favored : 89.72 % Rotamer: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.23), residues: 1197 helix: -0.09 (0.19), residues: 683 sheet: 0.76 (0.48), residues: 110 loop : -2.54 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 398 TYR 0.026 0.002 TYR B 98 PHE 0.037 0.003 PHE B 66 TRP 0.024 0.002 TRP D 38 HIS 0.033 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 ( 9970) covalent geometry : angle 0.82843 / 0.45 (13514) hydrogen bonds : bond 0.05990 / 4.14 ( 595) hydrogen bonds : angle 6.23797 / 4.54 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8560 (pmm) cc_final: 0.8296 (pmm) REVERT: A 44 TYR cc_start: 0.5784 (m-80) cc_final: 0.5539 (m-80) REVERT: A 79 LEU cc_start: 0.9070 (mm) cc_final: 0.8854 (mm) REVERT: A 98 TYR cc_start: 0.7683 (t80) cc_final: 0.7423 (t80) REVERT: A 109 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8432 (ttpp) REVERT: A 118 GLU cc_start: 0.8937 (pt0) cc_final: 0.8674 (pt0) REVERT: A 132 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8462 (mtm180) REVERT: A 153 PHE cc_start: 0.9181 (t80) cc_final: 0.8790 (t80) REVERT: A 179 HIS cc_start: 0.8456 (m-70) cc_final: 0.8058 (m-70) REVERT: A 204 MET cc_start: 0.8403 (tpp) cc_final: 0.7715 (tpp) REVERT: A 211 LYS cc_start: 0.9099 (mttt) cc_final: 0.8467 (mttt) REVERT: A 377 MET cc_start: 0.9164 (tmm) cc_final: 0.8840 (tmm) REVERT: B 54 GLN cc_start: 0.9552 (pp30) cc_final: 0.9149 (pp30) REVERT: B 55 LEU cc_start: 0.9201 (mt) cc_final: 0.8793 (mt) REVERT: B 74 LEU cc_start: 0.9355 (mt) cc_final: 0.9151 (mt) REVERT: B 78 CYS cc_start: 0.8691 (p) cc_final: 0.8425 (p) REVERT: B 179 HIS cc_start: 0.8742 (m-70) cc_final: 0.8447 (m-70) REVERT: B 189 THR cc_start: 0.6762 (p) cc_final: 0.5879 (p) REVERT: B 198 MET cc_start: 0.8456 (mmm) cc_final: 0.8045 (mmm) REVERT: B 307 ASN cc_start: 0.8292 (m110) cc_final: 0.7732 (t0) REVERT: B 340 TYR cc_start: 0.9004 (m-80) cc_final: 0.8647 (m-80) REVERT: B 344 ARG cc_start: 0.9243 (ttt-90) cc_final: 0.8710 (mtp180) REVERT: B 363 LEU cc_start: 0.9415 (mt) cc_final: 0.8975 (mt) REVERT: B 376 LEU cc_start: 0.9690 (mt) cc_final: 0.9171 (mt) REVERT: B 377 MET cc_start: 0.9598 (ttm) cc_final: 0.9151 (mtp) REVERT: B 380 HIS cc_start: 0.9050 (m90) cc_final: 0.8628 (m90) REVERT: C 42 TRP cc_start: 0.8616 (t60) cc_final: 0.8045 (t60) REVERT: C 58 HIS cc_start: 0.9217 (m170) cc_final: 0.8956 (m170) REVERT: C 76 PHE cc_start: 0.9151 (m-80) cc_final: 0.8885 (m-80) REVERT: C 86 THR cc_start: 0.8434 (m) cc_final: 0.8197 (p) REVERT: C 191 THR cc_start: 0.9208 (m) cc_final: 0.8662 (p) REVERT: C 200 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 213 LYS cc_start: 0.8902 (tttt) cc_final: 0.8563 (tmtt) REVERT: C 222 LEU cc_start: 0.9259 (pp) cc_final: 0.9045 (tt) REVERT: D 35 ILE cc_start: 0.8684 (tp) cc_final: 0.8455 (mp) REVERT: D 115 LEU cc_start: 0.9255 (mt) cc_final: 0.8651 (tt) REVERT: D 124 ASP cc_start: 0.9640 (m-30) cc_final: 0.9377 (m-30) REVERT: D 149 MET cc_start: 0.9266 (mpp) cc_final: 0.8741 (mpp) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.1024 time to fit residues: 48.2977 Evaluate side-chains 275 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 220 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.121397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.097186 restraints weight = 32294.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100322 restraints weight = 21905.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.102650 restraints weight = 16185.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104376 restraints weight = 12656.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.105635 restraints weight = 10386.506| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9970 Z= 0.219 Angle : 0.888 13.610 13514 Z= 0.477 Chirality : 0.048 0.255 1563 Planarity : 0.007 0.156 1689 Dihedral : 11.128 129.389 1464 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.61 % Favored : 88.97 % Rotamer: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.23), residues: 1197 helix: -0.29 (0.19), residues: 691 sheet: 0.73 (0.49), residues: 105 loop : -2.58 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 401 TYR 0.027 0.002 TYR B 98 PHE 0.037 0.003 PHE A 296 TRP 0.021 0.003 TRP D 69 HIS 0.030 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 ( 9970) covalent geometry : angle 0.88800 / 0.48 (13514) hydrogen bonds : bond 0.06092 / 4.22 ( 595) hydrogen bonds : angle 6.31236 / 4.60 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8677 (pmm) cc_final: 0.8401 (pmm) REVERT: A 54 GLN cc_start: 0.9379 (mt0) cc_final: 0.9061 (mm-40) REVERT: A 76 MET cc_start: 0.9227 (ptp) cc_final: 0.8971 (ppp) REVERT: A 77 LEU cc_start: 0.9222 (mt) cc_final: 0.8514 (mt) REVERT: A 79 LEU cc_start: 0.9082 (mm) cc_final: 0.8821 (mm) REVERT: A 98 TYR cc_start: 0.7758 (t80) cc_final: 0.7425 (t80) REVERT: A 109 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8442 (ttpp) REVERT: A 132 ARG cc_start: 0.8745 (mtm110) cc_final: 0.8430 (mtm180) REVERT: A 153 PHE cc_start: 0.9195 (t80) cc_final: 0.8841 (t80) REVERT: A 179 HIS cc_start: 0.8484 (m-70) cc_final: 0.8145 (m-70) REVERT: A 204 MET cc_start: 0.8566 (tpp) cc_final: 0.7962 (tpp) REVERT: A 211 LYS cc_start: 0.9149 (mttt) cc_final: 0.8707 (mttt) REVERT: A 377 MET cc_start: 0.9106 (tmm) cc_final: 0.8840 (tmm) REVERT: B 55 LEU cc_start: 0.9167 (mt) cc_final: 0.8878 (mt) REVERT: B 74 LEU cc_start: 0.9395 (mt) cc_final: 0.9175 (mt) REVERT: B 78 CYS cc_start: 0.8723 (p) cc_final: 0.8449 (p) REVERT: B 100 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8364 (mm-30) REVERT: B 137 MET cc_start: 0.8686 (tpt) cc_final: 0.8476 (tpt) REVERT: B 170 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8765 (tm-30) REVERT: B 192 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6577 (mp10) REVERT: B 196 HIS cc_start: 0.8251 (m-70) cc_final: 0.7868 (m-70) REVERT: B 198 MET cc_start: 0.8495 (mmm) cc_final: 0.8119 (mmm) REVERT: B 307 ASN cc_start: 0.8191 (m110) cc_final: 0.7590 (t0) REVERT: B 338 GLU cc_start: 0.8171 (mp0) cc_final: 0.7621 (pp20) REVERT: B 363 LEU cc_start: 0.9369 (mt) cc_final: 0.9044 (mt) REVERT: B 370 ASP cc_start: 0.8786 (t0) cc_final: 0.8346 (p0) REVERT: B 376 LEU cc_start: 0.9695 (mt) cc_final: 0.9222 (mt) REVERT: B 380 HIS cc_start: 0.9063 (m90) cc_final: 0.8541 (m90) REVERT: B 396 THR cc_start: 0.9756 (m) cc_final: 0.9538 (p) REVERT: B 400 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9110 (mm-30) REVERT: C 76 PHE cc_start: 0.9176 (m-80) cc_final: 0.8931 (m-80) REVERT: C 149 MET cc_start: 0.6073 (ptt) cc_final: 0.5778 (ppp) REVERT: C 159 LYS cc_start: 0.7856 (mttt) cc_final: 0.7645 (tptp) REVERT: C 160 PHE cc_start: 0.8598 (t80) cc_final: 0.8277 (t80) REVERT: C 198 LEU cc_start: 0.9170 (tp) cc_final: 0.8943 (tp) REVERT: C 200 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8814 (mt-10) REVERT: C 213 LYS cc_start: 0.8958 (tttt) cc_final: 0.8639 (tmtt) REVERT: C 222 LEU cc_start: 0.9276 (pp) cc_final: 0.9031 (tt) REVERT: D 38 TRP cc_start: 0.6923 (m100) cc_final: 0.6716 (m-90) REVERT: D 104 ASP cc_start: 0.8776 (t0) cc_final: 0.8356 (t0) REVERT: D 109 GLN cc_start: 0.8223 (tt0) cc_final: 0.7811 (mt0) REVERT: D 115 LEU cc_start: 0.9214 (mt) cc_final: 0.8641 (tt) REVERT: D 124 ASP cc_start: 0.9691 (m-30) cc_final: 0.9458 (m-30) REVERT: D 149 MET cc_start: 0.9159 (mpp) cc_final: 0.8557 (mpp) REVERT: D 167 LEU cc_start: 0.6460 (tp) cc_final: 0.5800 (tt) REVERT: D 200 GLU cc_start: 0.8555 (tt0) cc_final: 0.8155 (mm-30) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.0984 time to fit residues: 45.7406 Evaluate side-chains 279 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 0.0040 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099814 restraints weight = 31806.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102988 restraints weight = 21285.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.105384 restraints weight = 15563.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107105 restraints weight = 12060.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108507 restraints weight = 9842.515| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9970 Z= 0.185 Angle : 0.862 13.171 13514 Z= 0.466 Chirality : 0.048 0.256 1563 Planarity : 0.007 0.154 1689 Dihedral : 11.000 127.305 1464 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.77 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.23), residues: 1197 helix: -0.21 (0.19), residues: 694 sheet: 0.70 (0.49), residues: 106 loop : -2.53 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 95 TYR 0.025 0.002 TYR B 98 PHE 0.038 0.003 PHE A 201 TRP 0.020 0.002 TRP D 69 HIS 0.033 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 ( 9970) covalent geometry : angle 0.86185 / 0.47 (13514) hydrogen bonds : bond 0.05921 / 4.08 ( 595) hydrogen bonds : angle 6.30062 / 4.60 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8700 (pmm) cc_final: 0.8388 (pmm) REVERT: A 54 GLN cc_start: 0.9397 (mt0) cc_final: 0.9093 (mm-40) REVERT: A 76 MET cc_start: 0.9159 (ptp) cc_final: 0.8798 (ppp) REVERT: A 77 LEU cc_start: 0.9201 (mt) cc_final: 0.8468 (mt) REVERT: A 98 TYR cc_start: 0.7657 (t80) cc_final: 0.7394 (t80) REVERT: A 109 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8426 (ttpp) REVERT: A 153 PHE cc_start: 0.9197 (t80) cc_final: 0.8826 (t80) REVERT: A 179 HIS cc_start: 0.8402 (m-70) cc_final: 0.8084 (m-70) REVERT: A 204 MET cc_start: 0.8415 (tpp) cc_final: 0.7712 (tpp) REVERT: A 211 LYS cc_start: 0.9092 (mttt) cc_final: 0.8597 (mttt) REVERT: A 377 MET cc_start: 0.9034 (tmm) cc_final: 0.8790 (tmm) REVERT: B 55 LEU cc_start: 0.9166 (mt) cc_final: 0.8915 (mt) REVERT: B 100 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8383 (mm-30) REVERT: B 179 HIS cc_start: 0.8680 (m-70) cc_final: 0.8368 (m-70) REVERT: B 187 TYR cc_start: 0.8024 (t80) cc_final: 0.7700 (t80) REVERT: B 196 HIS cc_start: 0.8029 (m-70) cc_final: 0.7819 (m-70) REVERT: B 197 MET cc_start: 0.6920 (ptp) cc_final: 0.5927 (ptp) REVERT: B 198 MET cc_start: 0.8441 (mmm) cc_final: 0.8136 (mmm) REVERT: B 201 PHE cc_start: 0.8544 (m-80) cc_final: 0.7695 (m-80) REVERT: B 252 ASP cc_start: 0.9096 (t0) cc_final: 0.8894 (t0) REVERT: B 307 ASN cc_start: 0.8239 (m110) cc_final: 0.7737 (t0) REVERT: B 340 TYR cc_start: 0.9061 (m-80) cc_final: 0.8584 (m-80) REVERT: B 344 ARG cc_start: 0.9147 (ttt-90) cc_final: 0.8485 (mtp180) REVERT: B 363 LEU cc_start: 0.9414 (mt) cc_final: 0.9052 (mt) REVERT: B 376 LEU cc_start: 0.9690 (mt) cc_final: 0.9163 (mt) REVERT: B 380 HIS cc_start: 0.8959 (m90) cc_final: 0.8559 (m90) REVERT: B 396 THR cc_start: 0.9772 (m) cc_final: 0.9543 (p) REVERT: B 400 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9118 (mm-30) REVERT: C 48 ASP cc_start: 0.7878 (p0) cc_final: 0.7505 (p0) REVERT: C 213 LYS cc_start: 0.8899 (tttt) cc_final: 0.8569 (tmtt) REVERT: D 95 ARG cc_start: 0.7798 (ptt180) cc_final: 0.7552 (ptt180) REVERT: D 115 LEU cc_start: 0.9126 (mt) cc_final: 0.8575 (tp) REVERT: D 119 LEU cc_start: 0.9636 (mt) cc_final: 0.9364 (mt) REVERT: D 124 ASP cc_start: 0.9665 (m-30) cc_final: 0.9409 (m-30) REVERT: D 149 MET cc_start: 0.9192 (mpp) cc_final: 0.8532 (mpp) REVERT: D 200 GLU cc_start: 0.8732 (tt0) cc_final: 0.8336 (mm-30) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.0938 time to fit residues: 44.8497 Evaluate side-chains 278 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN D 186 HIS ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.122896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098444 restraints weight = 31772.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.101591 restraints weight = 21261.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103937 restraints weight = 15578.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.105680 restraints weight = 12156.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107017 restraints weight = 9947.319| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9970 Z= 0.194 Angle : 0.883 16.307 13514 Z= 0.471 Chirality : 0.049 0.298 1563 Planarity : 0.007 0.153 1689 Dihedral : 10.953 127.070 1464 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.86 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.23), residues: 1197 helix: -0.35 (0.19), residues: 696 sheet: 0.68 (0.50), residues: 102 loop : -2.51 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 132 TYR 0.025 0.002 TYR B 98 PHE 0.038 0.003 PHE A 296 TRP 0.022 0.002 TRP B 191 HIS 0.026 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 9970) covalent geometry : angle 0.88324 / 0.47 (13514) hydrogen bonds : bond 0.05942 / 4.11 ( 595) hydrogen bonds : angle 6.34373 / 4.61 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8780 (pmm) cc_final: 0.8469 (pmm) REVERT: A 44 TYR cc_start: 0.5785 (m-80) cc_final: 0.5401 (m-80) REVERT: A 109 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8383 (ttpp) REVERT: A 128 LYS cc_start: 0.9109 (pptt) cc_final: 0.8885 (pptt) REVERT: A 132 ARG cc_start: 0.8455 (ptt-90) cc_final: 0.8242 (mtm180) REVERT: A 153 PHE cc_start: 0.9169 (t80) cc_final: 0.8694 (t80) REVERT: A 179 HIS cc_start: 0.8331 (m-70) cc_final: 0.8053 (m-70) REVERT: A 200 ILE cc_start: 0.9514 (tp) cc_final: 0.9273 (tt) REVERT: A 204 MET cc_start: 0.8481 (tpp) cc_final: 0.7871 (tpp) REVERT: A 211 LYS cc_start: 0.9069 (mttt) cc_final: 0.8545 (mttm) REVERT: A 217 GLN cc_start: 0.9413 (mp10) cc_final: 0.9210 (mp10) REVERT: A 377 MET cc_start: 0.9083 (tmm) cc_final: 0.8810 (tmm) REVERT: A 384 ASN cc_start: 0.9682 (m110) cc_final: 0.9369 (m110) REVERT: B 19 MET cc_start: 0.7775 (pmm) cc_final: 0.6750 (pmm) REVERT: B 20 ASP cc_start: 0.8026 (m-30) cc_final: 0.7046 (m-30) REVERT: B 55 LEU cc_start: 0.9159 (mt) cc_final: 0.8912 (mt) REVERT: B 66 PHE cc_start: 0.6892 (t80) cc_final: 0.6687 (t80) REVERT: B 88 LYS cc_start: 0.9448 (tttt) cc_final: 0.9104 (tptp) REVERT: B 100 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8442 (mm-30) REVERT: B 179 HIS cc_start: 0.8656 (m-70) cc_final: 0.8305 (m-70) REVERT: B 187 TYR cc_start: 0.7993 (t80) cc_final: 0.7588 (t80) REVERT: B 196 HIS cc_start: 0.8133 (m-70) cc_final: 0.7867 (m-70) REVERT: B 198 MET cc_start: 0.8590 (mmm) cc_final: 0.8192 (mmm) REVERT: B 252 ASP cc_start: 0.9140 (t0) cc_final: 0.8921 (t0) REVERT: B 307 ASN cc_start: 0.8241 (m110) cc_final: 0.7772 (t0) REVERT: B 344 ARG cc_start: 0.9176 (ttt-90) cc_final: 0.8570 (mtp180) REVERT: B 363 LEU cc_start: 0.9416 (mt) cc_final: 0.9054 (mt) REVERT: B 376 LEU cc_start: 0.9683 (mt) cc_final: 0.9161 (mt) REVERT: B 380 HIS cc_start: 0.8982 (m90) cc_final: 0.8534 (m90) REVERT: B 400 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9077 (mm-30) REVERT: C 42 TRP cc_start: 0.8636 (t60) cc_final: 0.8082 (t60) REVERT: C 159 LYS cc_start: 0.7835 (mttt) cc_final: 0.7632 (tptp) REVERT: C 213 LYS cc_start: 0.8906 (tttt) cc_final: 0.8603 (tmtt) REVERT: C 218 LYS cc_start: 0.7291 (mppt) cc_final: 0.5832 (mppt) REVERT: D 104 ASP cc_start: 0.8805 (t0) cc_final: 0.8119 (t0) REVERT: D 109 GLN cc_start: 0.8358 (tt0) cc_final: 0.7917 (mt0) REVERT: D 124 ASP cc_start: 0.9663 (m-30) cc_final: 0.9414 (m-30) REVERT: D 136 MET cc_start: 0.7561 (mmm) cc_final: 0.6515 (mmm) REVERT: D 149 MET cc_start: 0.9151 (mpp) cc_final: 0.8547 (mpp) REVERT: D 200 GLU cc_start: 0.8626 (tt0) cc_final: 0.8242 (mm-30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.0975 time to fit residues: 45.7173 Evaluate side-chains 281 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 146 ASN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.126013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100901 restraints weight = 31389.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.104095 restraints weight = 21186.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.106456 restraints weight = 15644.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108249 restraints weight = 12269.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.109649 restraints weight = 10064.496| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9970 Z= 0.179 Angle : 0.882 18.810 13514 Z= 0.469 Chirality : 0.049 0.268 1563 Planarity : 0.007 0.153 1689 Dihedral : 10.836 127.324 1464 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.61 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.24), residues: 1197 helix: -0.30 (0.19), residues: 700 sheet: 0.69 (0.49), residues: 102 loop : -2.47 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 132 TYR 0.025 0.002 TYR B 98 PHE 0.043 0.003 PHE B 66 TRP 0.026 0.002 TRP B 191 HIS 0.021 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 9970) covalent geometry : angle 0.88200 / 0.47 (13514) hydrogen bonds : bond 0.05699 / 3.92 ( 595) hydrogen bonds : angle 6.33494 / 4.62 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8784 (pmm) cc_final: 0.8484 (pmm) REVERT: A 54 GLN cc_start: 0.9311 (mt0) cc_final: 0.9099 (mm-40) REVERT: A 76 MET cc_start: 0.9174 (ptp) cc_final: 0.8851 (ppp) REVERT: A 77 LEU cc_start: 0.9147 (mt) cc_final: 0.8434 (mt) REVERT: A 109 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8327 (ttpp) REVERT: A 153 PHE cc_start: 0.9112 (t80) cc_final: 0.8747 (t80) REVERT: A 179 HIS cc_start: 0.8184 (m-70) cc_final: 0.7951 (m-70) REVERT: A 200 ILE cc_start: 0.9428 (tp) cc_final: 0.9110 (tt) REVERT: A 204 MET cc_start: 0.8532 (tpp) cc_final: 0.7857 (tpp) REVERT: A 209 LEU cc_start: 0.9460 (pt) cc_final: 0.9217 (pp) REVERT: A 211 LYS cc_start: 0.9055 (mttt) cc_final: 0.8518 (mttt) REVERT: A 217 GLN cc_start: 0.9355 (mp10) cc_final: 0.9138 (mp10) REVERT: A 248 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8535 (ttpt) REVERT: A 252 ASP cc_start: 0.9313 (m-30) cc_final: 0.9102 (m-30) REVERT: A 377 MET cc_start: 0.9065 (tmm) cc_final: 0.8828 (tmm) REVERT: A 384 ASN cc_start: 0.9654 (m110) cc_final: 0.9343 (m110) REVERT: B 19 MET cc_start: 0.7717 (pmm) cc_final: 0.6705 (pmm) REVERT: B 20 ASP cc_start: 0.7885 (m-30) cc_final: 0.7005 (m-30) REVERT: B 55 LEU cc_start: 0.9134 (mt) cc_final: 0.8895 (mt) REVERT: B 88 LYS cc_start: 0.9455 (tttt) cc_final: 0.9091 (tptp) REVERT: B 100 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8434 (mm-30) REVERT: B 170 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 179 HIS cc_start: 0.8631 (m-70) cc_final: 0.8327 (m-70) REVERT: B 187 TYR cc_start: 0.7755 (t80) cc_final: 0.7258 (t80) REVERT: B 196 HIS cc_start: 0.8121 (m-70) cc_final: 0.7744 (m-70) REVERT: B 198 MET cc_start: 0.8501 (mmm) cc_final: 0.8055 (mmm) REVERT: B 252 ASP cc_start: 0.9140 (t0) cc_final: 0.8914 (t0) REVERT: B 298 ARG cc_start: 0.8778 (tpp80) cc_final: 0.8170 (mmm160) REVERT: B 307 ASN cc_start: 0.8093 (m110) cc_final: 0.7797 (t0) REVERT: B 344 ARG cc_start: 0.9217 (ttt-90) cc_final: 0.8614 (mtp180) REVERT: B 363 LEU cc_start: 0.9414 (mt) cc_final: 0.9041 (mt) REVERT: B 376 LEU cc_start: 0.9691 (mt) cc_final: 0.9181 (mt) REVERT: B 380 HIS cc_start: 0.8985 (m90) cc_final: 0.8550 (m90) REVERT: B 400 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9110 (mm-30) REVERT: C 42 TRP cc_start: 0.8546 (t60) cc_final: 0.7960 (t60) REVERT: C 213 LYS cc_start: 0.8828 (tttt) cc_final: 0.8490 (tmtt) REVERT: C 218 LYS cc_start: 0.7417 (mppt) cc_final: 0.6034 (mppt) REVERT: D 124 ASP cc_start: 0.9634 (m-30) cc_final: 0.9406 (m-30) REVERT: D 149 MET cc_start: 0.9086 (mpp) cc_final: 0.8384 (mpp) REVERT: D 200 GLU cc_start: 0.8693 (tt0) cc_final: 0.8352 (mm-30) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.0976 time to fit residues: 46.5827 Evaluate side-chains 283 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 79 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.124387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099627 restraints weight = 31932.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.102801 restraints weight = 21400.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.105144 restraints weight = 15703.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.106942 restraints weight = 12278.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108312 restraints weight = 10031.771| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.7456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9970 Z= 0.183 Angle : 0.893 15.801 13514 Z= 0.470 Chirality : 0.049 0.273 1563 Planarity : 0.007 0.152 1689 Dihedral : 10.807 126.631 1464 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.27 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.24), residues: 1197 helix: -0.26 (0.19), residues: 694 sheet: 0.73 (0.49), residues: 102 loop : -2.53 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 132 TYR 0.025 0.002 TYR B 98 PHE 0.034 0.003 PHE B 66 TRP 0.025 0.002 TRP B 191 HIS 0.024 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 9970) covalent geometry : angle 0.89251 / 0.47 (13514) hydrogen bonds : bond 0.05710 / 3.92 ( 595) hydrogen bonds : angle 6.33996 / 4.61 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.78 seconds wall clock time: 34 minutes 1.24 seconds (2041.24 seconds total)