Starting phenix.real_space_refine on Tue Mar 3 17:15:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6i_31481/03_2026/7f6i_31481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6i_31481/03_2026/7f6i_31481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f6i_31481/03_2026/7f6i_31481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6i_31481/03_2026/7f6i_31481.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f6i_31481/03_2026/7f6i_31481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6i_31481/03_2026/7f6i_31481.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 4724 2.51 5 N 1244 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7361 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2448 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 3, 'TRANS': 6} Chain: "B" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1867 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 1 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2507 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain: "D" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 371 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.65, per 1000 atoms: 0.22 Number of scatterers: 7361 At special positions: 0 Unit cell: (104.442, 94.302, 120.666, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1336 8.00 N 1244 7.00 C 4724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 211 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 199.1 milliseconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 45.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 50 through 85 removed outlier: 3.756A pdb=" N GLY A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.655A pdb=" N HIS A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 108 removed outlier: 3.663A pdb=" N TYR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 119 removed outlier: 3.946A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 160 removed outlier: 4.091A pdb=" N LEU A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.740A pdb=" N ARG A 169 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.594A pdb=" N LEU A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.892A pdb=" N GLU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.804A pdb=" N MET A 256 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 257 " --> pdb=" O ASN A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 257' Processing helix chain 'A' and resid 264 through 298 removed outlier: 3.973A pdb=" N ALA A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 303 through 321 removed outlier: 4.061A pdb=" N PHE A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.815A pdb=" N CYS A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'B' and resid 15 through 36 Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 212 through 217 removed outlier: 4.061A pdb=" N TRP B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 246 through 261 removed outlier: 3.615A pdb=" N TYR B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 removed outlier: 3.566A pdb=" N GLN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.695A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.542A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 201 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196 removed outlier: 6.444A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N SER B 225 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LYS B 41 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N MET B 227 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 43 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 229 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 45 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ALA B 231 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.761A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.656A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.852A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.646A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.621A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.931A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1041 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: 1.24 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2361 1.34 - 1.46: 1415 1.46 - 1.58: 3658 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 7518 Sorted by residual: bond pdb=" C10 CLR A 503 " pdb=" C5 CLR A 503 " ideal model delta sigma weight residual 1.519 1.401 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C10 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C4 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.506 1.392 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C10 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C4 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.506 1.395 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 7513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 9606 1.82 - 3.64: 511 3.64 - 5.47: 63 5.47 - 7.29: 21 7.29 - 9.11: 4 Bond angle restraints: 10205 Sorted by residual: angle pdb=" N PHE A 259 " pdb=" CA PHE A 259 " pdb=" C PHE A 259 " ideal model delta sigma weight residual 113.20 106.01 7.19 1.21e+00 6.83e-01 3.53e+01 angle pdb=" CA GLN B 197 " pdb=" C GLN B 197 " pdb=" O GLN B 197 " ideal model delta sigma weight residual 122.27 117.41 4.86 1.16e+00 7.43e-01 1.75e+01 angle pdb=" N ASN A 254 " pdb=" CA ASN A 254 " pdb=" C ASN A 254 " ideal model delta sigma weight residual 113.02 108.55 4.47 1.20e+00 6.94e-01 1.39e+01 angle pdb=" N GLU A 255 " pdb=" CA GLU A 255 " pdb=" C GLU A 255 " ideal model delta sigma weight residual 113.19 108.77 4.42 1.19e+00 7.06e-01 1.38e+01 angle pdb=" N VAL C 90 " pdb=" CA VAL C 90 " pdb=" C VAL C 90 " ideal model delta sigma weight residual 111.67 108.14 3.53 9.50e-01 1.11e+00 1.38e+01 ... (remaining 10200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 4426 24.42 - 48.83: 175 48.83 - 73.25: 26 73.25 - 97.67: 4 97.67 - 122.08: 3 Dihedral angle restraints: 4634 sinusoidal: 1965 harmonic: 2669 Sorted by residual: dihedral pdb=" CB CYS A 130 " pdb=" SG CYS A 130 " pdb=" SG CYS A 211 " pdb=" CB CYS A 211 " ideal model delta sinusoidal sigma weight residual -86.00 -170.09 84.09 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS A 47 " pdb=" SG CYS A 47 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 151.56 -58.56 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N TYR B 291 " pdb=" CA TYR B 291 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 4631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1053 0.094 - 0.189: 105 0.189 - 0.283: 8 0.283 - 0.377: 4 0.377 - 0.472: 6 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C14 CLR A 503 " pdb=" C13 CLR A 503 " pdb=" C15 CLR A 503 " pdb=" C8 CLR A 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" C14 CLR A 502 " pdb=" C13 CLR A 502 " pdb=" C15 CLR A 502 " pdb=" C8 CLR A 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C14 CLR A 501 " pdb=" C13 CLR A 501 " pdb=" C15 CLR A 501 " pdb=" C8 CLR A 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 1173 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 38 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO C 39 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 55 " -0.023 2.00e-02 2.50e+03 1.67e-02 4.90e+00 pdb=" CG PHE B 55 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 55 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 55 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 55 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 55 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 55 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 42 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ARG C 42 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG C 42 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 43 " 0.012 2.00e-02 2.50e+03 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1209 2.76 - 3.30: 6925 3.30 - 3.83: 12054 3.83 - 4.37: 14786 4.37 - 4.90: 25270 Nonbonded interactions: 60244 Sorted by model distance: nonbonded pdb=" OG1 THR A 314 " pdb=" NH2 ARG L 10 " model vdw 2.227 3.120 nonbonded pdb=" NE ARG C 251 " pdb=" OE2 GLU C 260 " model vdw 2.257 3.120 nonbonded pdb=" OG SER A 318 " pdb=" OG SER L 7 " model vdw 2.331 3.040 nonbonded pdb=" OG SER C 108 " pdb=" OD1 ASP C 154 " model vdw 2.368 3.040 nonbonded pdb=" OG SER C 147 " pdb=" O VAL C 187 " model vdw 2.400 3.040 ... (remaining 60239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.800 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.008 0.118 7520 Z= 0.437 Angle : 0.922 9.110 10209 Z= 0.554 Chirality : 0.067 0.472 1176 Planarity : 0.005 0.066 1270 Dihedral : 13.558 122.083 2894 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.50 % Allowed : 0.99 % Favored : 98.51 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 903 helix: 1.40 (0.26), residues: 387 sheet: -0.03 (0.39), residues: 184 loop : -1.26 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 19 TYR 0.014 0.002 TYR A 347 PHE 0.035 0.002 PHE B 55 TRP 0.018 0.002 TRP A 283 HIS 0.008 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 7518) covalent geometry : angle 0.92192 (10205) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.88931 ( 4) hydrogen bonds : bond 0.11764 ( 358) hydrogen bonds : angle 5.07715 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.315 Fit side-chains REVERT: C 340 ASN cc_start: 0.8017 (t0) cc_final: 0.7806 (t0) outliers start: 4 outliers final: 1 residues processed: 123 average time/residue: 0.6613 time to fit residues: 85.1715 Evaluate side-chains 86 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0020 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 254 ASN A 324 ASN B 265 GLN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122859 restraints weight = 8208.924| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.04 r_work: 0.3238 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7520 Z= 0.125 Angle : 0.556 6.725 10209 Z= 0.289 Chirality : 0.043 0.210 1176 Planarity : 0.004 0.055 1270 Dihedral : 8.644 90.715 1190 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.61 % Allowed : 10.19 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.28), residues: 903 helix: 2.16 (0.26), residues: 383 sheet: 0.23 (0.38), residues: 179 loop : -1.23 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 96 TYR 0.010 0.001 TYR B 291 PHE 0.023 0.001 PHE B 55 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7518) covalent geometry : angle 0.55562 (10205) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.47016 ( 4) hydrogen bonds : bond 0.04342 ( 358) hydrogen bonds : angle 4.04795 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.272 Fit side-chains REVERT: A 249 GLN cc_start: 0.8507 (tt0) cc_final: 0.8305 (tt0) REVERT: B 19 ARG cc_start: 0.7334 (mmm-85) cc_final: 0.6947 (tmt170) REVERT: B 31 ARG cc_start: 0.7228 (ttm-80) cc_final: 0.6770 (ttp-110) REVERT: D 21 MET cc_start: 0.5870 (tmm) cc_final: 0.5615 (tmm) outliers start: 13 outliers final: 5 residues processed: 110 average time/residue: 0.5465 time to fit residues: 63.6306 Evaluate side-chains 103 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119570 restraints weight = 8076.744| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.99 r_work: 0.3198 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7520 Z= 0.152 Angle : 0.581 8.514 10209 Z= 0.300 Chirality : 0.043 0.193 1176 Planarity : 0.004 0.048 1270 Dihedral : 7.223 59.655 1190 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.98 % Allowed : 11.68 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 903 helix: 2.36 (0.26), residues: 382 sheet: 0.20 (0.37), residues: 184 loop : -1.28 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.015 0.001 TYR A 177 PHE 0.022 0.002 PHE B 55 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7518) covalent geometry : angle 0.58084 (10205) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.61345 ( 4) hydrogen bonds : bond 0.04747 ( 358) hydrogen bonds : angle 4.01183 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.309 Fit side-chains REVERT: A 262 ILE cc_start: 0.7896 (mp) cc_final: 0.7482 (pp) REVERT: B 19 ARG cc_start: 0.7191 (mmm-85) cc_final: 0.6896 (mmt180) REVERT: B 31 ARG cc_start: 0.7246 (ttm-80) cc_final: 0.6780 (ttp-110) REVERT: C 217 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8016 (ppp) outliers start: 24 outliers final: 10 residues processed: 115 average time/residue: 0.5621 time to fit residues: 68.2137 Evaluate side-chains 105 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121964 restraints weight = 8229.523| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.12 r_work: 0.3240 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7520 Z= 0.127 Angle : 0.526 6.522 10209 Z= 0.277 Chirality : 0.042 0.196 1176 Planarity : 0.004 0.045 1270 Dihedral : 6.300 59.230 1190 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.73 % Allowed : 12.92 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 903 helix: 2.51 (0.26), residues: 382 sheet: 0.19 (0.37), residues: 184 loop : -1.28 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.018 0.001 TYR A 177 PHE 0.023 0.001 PHE B 55 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7518) covalent geometry : angle 0.52618 (10205) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.47565 ( 4) hydrogen bonds : bond 0.04228 ( 358) hydrogen bonds : angle 3.87741 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.276 Fit side-chains REVERT: A 249 GLN cc_start: 0.8350 (tt0) cc_final: 0.7940 (tp-100) REVERT: A 262 ILE cc_start: 0.7854 (mp) cc_final: 0.7502 (pp) REVERT: B 19 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6869 (mmt180) REVERT: B 31 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6706 (ttp-110) REVERT: C 217 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7800 (pp-130) REVERT: D 47 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7158 (mp0) outliers start: 22 outliers final: 12 residues processed: 110 average time/residue: 0.5087 time to fit residues: 59.4037 Evaluate side-chains 105 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121167 restraints weight = 8213.913| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.96 r_work: 0.3221 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7520 Z= 0.122 Angle : 0.517 6.183 10209 Z= 0.273 Chirality : 0.042 0.196 1176 Planarity : 0.004 0.041 1270 Dihedral : 6.215 59.378 1190 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.86 % Allowed : 13.66 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.28), residues: 903 helix: 2.60 (0.26), residues: 382 sheet: 0.06 (0.36), residues: 189 loop : -1.23 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.021 0.001 TYR A 177 PHE 0.024 0.001 PHE B 55 TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7518) covalent geometry : angle 0.51726 (10205) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.50399 ( 4) hydrogen bonds : bond 0.04103 ( 358) hydrogen bonds : angle 3.82066 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: A 249 GLN cc_start: 0.8339 (tt0) cc_final: 0.7910 (tp-100) REVERT: B 19 ARG cc_start: 0.7220 (mmm-85) cc_final: 0.6557 (mmm160) REVERT: B 31 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6713 (ttp-170) REVERT: B 249 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8099 (mm-30) REVERT: C 217 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7828 (pp-130) REVERT: D 47 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7181 (mp0) outliers start: 23 outliers final: 11 residues processed: 105 average time/residue: 0.5202 time to fit residues: 58.0021 Evaluate side-chains 103 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119576 restraints weight = 8217.773| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.96 r_work: 0.3199 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7520 Z= 0.139 Angle : 0.534 6.756 10209 Z= 0.281 Chirality : 0.043 0.192 1176 Planarity : 0.004 0.038 1270 Dihedral : 6.262 59.608 1190 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.23 % Allowed : 13.66 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.28), residues: 903 helix: 2.52 (0.26), residues: 382 sheet: -0.11 (0.36), residues: 189 loop : -1.12 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.023 0.001 TYR A 177 PHE 0.029 0.002 PHE B 55 TRP 0.012 0.001 TRP A 123 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7518) covalent geometry : angle 0.53418 (10205) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.73786 ( 4) hydrogen bonds : bond 0.04379 ( 358) hydrogen bonds : angle 3.88501 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.278 Fit side-chains REVERT: A 200 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: B 19 ARG cc_start: 0.7094 (mmm-85) cc_final: 0.6416 (mmm160) REVERT: B 31 ARG cc_start: 0.6994 (ttm-80) cc_final: 0.6602 (ttp-170) REVERT: B 249 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8055 (mm-30) REVERT: B 356 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: C 217 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7752 (pp-130) REVERT: D 47 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7146 (mp0) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 0.5235 time to fit residues: 60.5738 Evaluate side-chains 106 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.157893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121692 restraints weight = 8210.575| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.97 r_work: 0.3237 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7520 Z= 0.122 Angle : 0.520 6.269 10209 Z= 0.273 Chirality : 0.042 0.195 1176 Planarity : 0.004 0.047 1270 Dihedral : 6.179 59.527 1190 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.73 % Allowed : 14.78 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.28), residues: 903 helix: 2.64 (0.26), residues: 382 sheet: -0.11 (0.36), residues: 189 loop : -1.07 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 197 TYR 0.024 0.001 TYR A 177 PHE 0.020 0.001 PHE B 55 TRP 0.018 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7518) covalent geometry : angle 0.51964 (10205) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.58074 ( 4) hydrogen bonds : bond 0.04064 ( 358) hydrogen bonds : angle 3.78749 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: A 322 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: B 19 ARG cc_start: 0.6986 (mmm-85) cc_final: 0.6400 (mmm160) REVERT: B 31 ARG cc_start: 0.7044 (ttm-80) cc_final: 0.6695 (ttp-170) REVERT: B 197 GLN cc_start: 0.6564 (mt0) cc_final: 0.6076 (tt0) REVERT: C 217 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7851 (pp-130) REVERT: D 47 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7113 (mp0) outliers start: 22 outliers final: 13 residues processed: 106 average time/residue: 0.5208 time to fit residues: 58.6438 Evaluate side-chains 104 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120435 restraints weight = 8293.259| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.92 r_work: 0.3166 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7520 Z= 0.155 Angle : 0.559 7.201 10209 Z= 0.294 Chirality : 0.044 0.188 1176 Planarity : 0.004 0.049 1270 Dihedral : 6.302 59.734 1190 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 14.78 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.28), residues: 903 helix: 2.46 (0.27), residues: 382 sheet: -0.17 (0.36), residues: 189 loop : -1.09 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 197 TYR 0.026 0.002 TYR A 177 PHE 0.033 0.002 PHE B 55 TRP 0.019 0.001 TRP A 123 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7518) covalent geometry : angle 0.55936 (10205) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.81994 ( 4) hydrogen bonds : bond 0.04624 ( 358) hydrogen bonds : angle 3.94625 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.297 Fit side-chains REVERT: A 200 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: A 322 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: B 19 ARG cc_start: 0.6936 (mmm-85) cc_final: 0.6362 (mmm160) REVERT: B 31 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6733 (ttp-170) REVERT: B 197 GLN cc_start: 0.6661 (mt0) cc_final: 0.6115 (tt0) REVERT: B 356 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: C 217 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7861 (pp-130) REVERT: D 47 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7217 (mp0) outliers start: 23 outliers final: 13 residues processed: 109 average time/residue: 0.5585 time to fit residues: 64.2791 Evaluate side-chains 106 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 76 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120398 restraints weight = 8198.107| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.88 r_work: 0.3154 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7520 Z= 0.157 Angle : 0.574 7.235 10209 Z= 0.300 Chirality : 0.044 0.188 1176 Planarity : 0.004 0.051 1270 Dihedral : 6.375 59.508 1190 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.36 % Allowed : 16.15 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.28), residues: 903 helix: 2.40 (0.27), residues: 382 sheet: -0.24 (0.37), residues: 184 loop : -1.14 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 197 TYR 0.028 0.002 TYR A 177 PHE 0.033 0.002 PHE B 55 TRP 0.014 0.001 TRP A 123 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7518) covalent geometry : angle 0.57435 (10205) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.73669 ( 4) hydrogen bonds : bond 0.04656 ( 358) hydrogen bonds : angle 3.96826 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.338 Fit side-chains REVERT: A 200 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: A 322 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: B 19 ARG cc_start: 0.6838 (mmm-85) cc_final: 0.6355 (mmm160) REVERT: B 31 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6743 (ttp-170) REVERT: B 197 GLN cc_start: 0.6619 (mt0) cc_final: 0.6034 (tt0) REVERT: B 356 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: C 34 THR cc_start: 0.7481 (p) cc_final: 0.7261 (p) REVERT: C 217 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7859 (pp-130) REVERT: D 47 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7172 (mp0) outliers start: 19 outliers final: 14 residues processed: 103 average time/residue: 0.5630 time to fit residues: 61.4136 Evaluate side-chains 107 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122307 restraints weight = 8219.529| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.90 r_work: 0.3161 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7520 Z= 0.135 Angle : 0.549 6.457 10209 Z= 0.289 Chirality : 0.043 0.191 1176 Planarity : 0.004 0.054 1270 Dihedral : 6.301 59.388 1190 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.48 % Allowed : 15.90 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 903 helix: 2.49 (0.27), residues: 382 sheet: -0.26 (0.36), residues: 184 loop : -1.08 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 197 TYR 0.029 0.002 TYR A 177 PHE 0.036 0.002 PHE B 55 TRP 0.015 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7518) covalent geometry : angle 0.54936 (10205) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.56791 ( 4) hydrogen bonds : bond 0.04338 ( 358) hydrogen bonds : angle 3.90526 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.329 Fit side-chains REVERT: A 200 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: A 322 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: B 19 ARG cc_start: 0.6813 (mmm-85) cc_final: 0.6342 (mmm160) REVERT: B 31 ARG cc_start: 0.7150 (ttm-80) cc_final: 0.6763 (ttp-170) REVERT: B 356 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: C 34 THR cc_start: 0.7545 (p) cc_final: 0.7312 (p) REVERT: C 217 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7875 (pp-130) REVERT: D 47 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7146 (mp0) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 0.5468 time to fit residues: 61.9699 Evaluate side-chains 108 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121708 restraints weight = 8212.663| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.90 r_work: 0.3196 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7520 Z= 0.134 Angle : 0.560 7.354 10209 Z= 0.292 Chirality : 0.043 0.191 1176 Planarity : 0.004 0.044 1270 Dihedral : 6.283 58.855 1190 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.61 % Allowed : 16.27 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 903 helix: 2.49 (0.27), residues: 382 sheet: -0.28 (0.36), residues: 183 loop : -1.06 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 197 TYR 0.030 0.002 TYR A 177 PHE 0.032 0.002 PHE B 55 TRP 0.014 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7518) covalent geometry : angle 0.55973 (10205) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.55991 ( 4) hydrogen bonds : bond 0.04324 ( 358) hydrogen bonds : angle 3.90644 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.45 seconds wall clock time: 48 minutes 35.01 seconds (2915.01 seconds total)