Starting phenix.real_space_refine on Thu Jul 2 07:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f6i_31481/07_2026/7f6i_31481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6i_31481/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_2026/7f6i_31481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_2026/7f6i_31481.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_2026/7f6i_31481.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_2026/7f6i_31481.cif" model { file = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_2026/7f6i_31481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_2026/7f6i_31481.cif" } 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-6108/lib/python3.11/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: 1.84, per 1000 atoms: 0.25 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: 0.62 Conformation dependent library (CDL) restraints added in 470.7 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: 0.21 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: 1.20 Time building geometry restraints manager: 0.84 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: 4283 24.42 - 48.83: 159 48.83 - 73.25: 19 73.25 - 97.67: 4 97.67 - 122.08: 1 Dihedral angle restraints: 4466 sinusoidal: 1797 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 4463 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: 1.200 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 12.849 122.083 2726 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/Z covalent geometry : bond 0.00794 / 0.44 ( 7518) covalent geometry : angle 0.92192 / 0.55 (10205) SS BOND : bond 0.00259 / 0.12 ( 2) SS BOND : angle 0.88931 / 0.35 ( 4) hydrogen bonds : bond 0.11764 / 7.95 ( 358) hydrogen bonds : angle 5.07715 / 3.81 ( 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 : 0.181 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: 0.5994 time to fit residues: 77.2532 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 : 0.238 ------------------------------------------------------------------------------- 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... 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 = 0.3826 r_free = 0.3826 target = 0.160449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124061 restraints weight = 8205.605| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.08 r_work: 0.3237 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7520 Z= 0.125 Angle : 0.549 6.780 10209 Z= 0.288 Chirality : 0.042 0.195 1176 Planarity : 0.004 0.055 1270 Dihedral : 6.576 108.987 1022 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.02 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: 0.82 (0.27), residues: 903 helix: 2.21 (0.26), residues: 380 sheet: 0.23 (0.38), residues: 179 loop : -1.23 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 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/Z covalent geometry : bond 0.00271 / 0.12 ( 7518) covalent geometry : angle 0.54940 / 0.29 (10205) SS BOND : bond 0.00194 / 0.09 ( 2) SS BOND : angle 0.47834 / 0.21 ( 4) hydrogen bonds : bond 0.04414 / 3.02 ( 358) hydrogen bonds : angle 4.05898 / 3.02 ( 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 : 0.276 Fit side-chains REVERT: B 19 ARG cc_start: 0.7338 (mmm-85) cc_final: 0.6949 (tmt170) REVERT: D 21 MET cc_start: 0.5903 (tmm) cc_final: 0.5611 (tmm) outliers start: 13 outliers final: 5 residues processed: 110 average time/residue: 0.4973 time to fit residues: 58.0122 Evaluate side-chains 105 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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: 0.7980 chunk 55 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 315 GLN A 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.158368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120166 restraints weight = 8059.461| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.98 r_work: 0.3216 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1736 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 : 0.532 6.116 10209 Z= 0.279 Chirality : 0.042 0.186 1176 Planarity : 0.004 0.048 1270 Dihedral : 6.310 103.472 1022 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.86 % Allowed : 11.80 % 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: 1.05 (0.28), residues: 903 helix: 2.46 (0.26), residues: 383 sheet: 0.28 (0.37), residues: 184 loop : -1.21 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.017 0.001 TYR A 177 PHE 0.020 0.001 PHE B 55 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7518) covalent geometry : angle 0.53162 / 0.28 (10205) SS BOND : bond 0.00208 / 0.10 ( 2) SS BOND : angle 0.43510 / 0.19 ( 4) hydrogen bonds : bond 0.04263 / 2.93 ( 358) hydrogen bonds : angle 3.88477 / 2.89 ( 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 123 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.224 Fit side-chains REVERT: A 262 ILE cc_start: 0.7881 (mp) cc_final: 0.7469 (pp) REVERT: B 19 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6824 (mmt180) REVERT: C 152 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8529 (tt) REVERT: C 217 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7842 (pp-130) outliers start: 23 outliers final: 9 residues processed: 112 average time/residue: 0.4565 time to fit residues: 54.2470 Evaluate side-chains 100 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN 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 C residue 123 ILE Chi-restraints excluded: chain C residue 152 LEU 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: 4.9990 chunk 87 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.0170 chunk 63 optimal weight: 0.8980 chunk 14 optimal weight: 0.0470 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124406 restraints weight = 8216.717| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.91 r_work: 0.3227 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1964 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= 0.115 Angle : 0.515 5.803 10209 Z= 0.271 Chirality : 0.041 0.190 1176 Planarity : 0.004 0.044 1270 Dihedral : 6.198 102.751 1022 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.11 % Allowed : 12.55 % 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: 1.10 (0.28), residues: 903 helix: 2.58 (0.26), residues: 385 sheet: 0.14 (0.37), residues: 184 loop : -1.19 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.019 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/Z covalent geometry : bond 0.00251 / 0.11 ( 7518) covalent geometry : angle 0.51528 / 0.27 (10205) SS BOND : bond 0.00197 / 0.09 ( 2) SS BOND : angle 0.41310 / 0.18 ( 4) hydrogen bonds : bond 0.03959 / 2.73 ( 358) hydrogen bonds : angle 3.78363 / 2.82 ( 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: 25 poor density : 96 time to evaluate : 0.289 Fit side-chains REVERT: A 262 ILE cc_start: 0.7831 (mp) cc_final: 0.7471 (pp) REVERT: B 19 ARG cc_start: 0.7164 (mmm-85) cc_final: 0.6891 (mmt180) REVERT: C 217 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7890 (pp-130) REVERT: D 47 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7128 (mp0) outliers start: 25 outliers final: 11 residues processed: 109 average time/residue: 0.4936 time to fit residues: 57.2171 Evaluate side-chains 105 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN 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 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 184 THR 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: 0.9980 chunk 34 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 GLN A 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124489 restraints weight = 8215.692| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.93 r_work: 0.3230 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7520 Z= 0.114 Angle : 0.505 5.802 10209 Z= 0.266 Chirality : 0.041 0.187 1176 Planarity : 0.004 0.041 1270 Dihedral : 6.136 101.991 1022 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.86 % Allowed : 13.91 % Favored : 83.23 % 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: 1.20 (0.28), residues: 903 helix: 2.76 (0.26), residues: 379 sheet: -0.02 (0.36), residues: 189 loop : -1.08 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 31 TYR 0.020 0.001 TYR A 177 PHE 0.027 0.001 PHE B 55 TRP 0.011 0.001 TRP A 123 HIS 0.002 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7518) covalent geometry : angle 0.50532 / 0.27 (10205) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 0.49303 / 0.21 ( 4) hydrogen bonds : bond 0.03911 / 2.69 ( 358) hydrogen bonds : angle 3.74535 / 2.79 ( 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 : 0.199 Fit side-chains REVERT: A 249 GLN cc_start: 0.8347 (tt0) cc_final: 0.7955 (tp-100) REVERT: A 262 ILE cc_start: 0.7791 (mp) cc_final: 0.7456 (pp) REVERT: B 19 ARG cc_start: 0.7229 (mmm-85) cc_final: 0.6573 (mmm160) REVERT: B 356 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: C 217 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7892 (pp-130) REVERT: D 47 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7135 (mp0) outliers start: 23 outliers final: 13 residues processed: 105 average time/residue: 0.4538 time to fit residues: 50.5648 Evaluate side-chains 108 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN 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 277 SER Chi-restraints excluded: chain C residue 322 ASP 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: 0.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120675 restraints weight = 8202.370| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.95 r_work: 0.3208 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2147 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= 0.136 Angle : 0.534 6.520 10209 Z= 0.279 Chirality : 0.042 0.183 1176 Planarity : 0.004 0.038 1270 Dihedral : 6.241 100.370 1022 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.86 % Allowed : 14.41 % Favored : 82.73 % 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: 1.10 (0.28), residues: 903 helix: 2.64 (0.26), residues: 382 sheet: -0.09 (0.36), residues: 189 loop : -1.08 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 31 TYR 0.021 0.001 TYR A 177 PHE 0.023 0.002 PHE B 55 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7518) covalent geometry : angle 0.53353 / 0.28 (10205) SS BOND : bond 0.00225 / 0.11 ( 2) SS BOND : angle 0.62163 / 0.26 ( 4) hydrogen bonds : bond 0.04308 / 2.96 ( 358) hydrogen bonds : angle 3.84165 / 2.87 ( 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 120 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.199 Fit side-chains REVERT: A 200 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: A 249 GLN cc_start: 0.8379 (tt0) cc_final: 0.7946 (tp-100) REVERT: B 19 ARG cc_start: 0.7119 (mmm-85) cc_final: 0.6464 (mmm160) REVERT: B 356 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: C 217 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7896 (pp-130) REVERT: D 47 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7178 (mp0) outliers start: 23 outliers final: 12 residues processed: 106 average time/residue: 0.5068 time to fit residues: 57.1198 Evaluate side-chains 107 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 229 ASN 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118111 restraints weight = 8254.660| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.91 r_work: 0.3142 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7520 Z= 0.204 Angle : 0.624 8.482 10209 Z= 0.324 Chirality : 0.045 0.174 1176 Planarity : 0.005 0.048 1270 Dihedral : 6.552 95.282 1022 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.86 % Allowed : 14.53 % Favored : 82.61 % 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: 0.77 (0.28), residues: 903 helix: 2.24 (0.26), residues: 382 sheet: -0.19 (0.37), residues: 186 loop : -1.13 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 197 TYR 0.024 0.002 TYR A 177 PHE 0.032 0.002 PHE B 55 TRP 0.013 0.002 TRP C 82 HIS 0.005 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 ( 7518) covalent geometry : angle 0.62331 / 0.32 (10205) SS BOND : bond 0.00226 / 0.11 ( 2) SS BOND : angle 1.15559 / 0.48 ( 4) hydrogen bonds : bond 0.05328 / 3.65 ( 358) hydrogen bonds : angle 4.14546 / 3.09 ( 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 117 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.231 Fit side-chains REVERT: A 200 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: A 249 GLN cc_start: 0.8392 (tt0) cc_final: 0.7928 (tp-100) REVERT: B 19 ARG cc_start: 0.6976 (mmm-85) cc_final: 0.6480 (mmm160) REVERT: B 49 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6642 (mm-30) REVERT: B 197 GLN cc_start: 0.6634 (mt0) cc_final: 0.6123 (tt0) REVERT: B 356 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: C 217 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8172 (ppp) REVERT: D 47 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7279 (mp0) outliers start: 23 outliers final: 9 residues processed: 105 average time/residue: 0.5140 time to fit residues: 57.2001 Evaluate side-chains 103 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 275 VAL 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 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 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: 1.9990 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120361 restraints weight = 8280.107| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.91 r_work: 0.3178 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7520 Z= 0.143 Angle : 0.550 6.710 10209 Z= 0.288 Chirality : 0.043 0.182 1176 Planarity : 0.004 0.048 1270 Dihedral : 6.357 97.886 1022 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.36 % Allowed : 15.78 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.28), residues: 903 helix: 2.42 (0.26), residues: 382 sheet: -0.22 (0.36), residues: 189 loop : -1.11 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 197 TYR 0.027 0.002 TYR A 177 PHE 0.032 0.002 PHE B 55 TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7518) covalent geometry : angle 0.55013 / 0.29 (10205) SS BOND : bond 0.00247 / 0.12 ( 2) SS BOND : angle 0.64402 / 0.27 ( 4) hydrogen bonds : bond 0.04451 / 3.06 ( 358) hydrogen bonds : angle 3.95277 / 2.95 ( 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 117 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.187 Fit side-chains REVERT: A 200 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: A 249 GLN cc_start: 0.8365 (tt0) cc_final: 0.7916 (tp-100) REVERT: A 322 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 19 ARG cc_start: 0.6952 (mmm-85) cc_final: 0.6464 (mmm160) REVERT: B 197 GLN cc_start: 0.6690 (mt0) cc_final: 0.6130 (tt0) REVERT: B 249 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8136 (mm-30) REVERT: B 356 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: C 34 THR cc_start: 0.7417 (p) cc_final: 0.7217 (p) REVERT: C 217 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7913 (pp-130) REVERT: D 47 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7165 (mp0) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 0.4868 time to fit residues: 56.5483 Evaluate side-chains 104 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.8980 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120343 restraints weight = 8197.314| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.89 r_work: 0.3148 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7520 Z= 0.173 Angle : 0.592 7.537 10209 Z= 0.309 Chirality : 0.044 0.177 1176 Planarity : 0.004 0.053 1270 Dihedral : 6.452 96.399 1022 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 0.79 (0.28), residues: 903 helix: 2.28 (0.26), residues: 382 sheet: -0.26 (0.36), residues: 189 loop : -1.11 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 31 TYR 0.029 0.002 TYR A 177 PHE 0.032 0.002 PHE B 55 TRP 0.017 0.001 TRP A 123 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 7518) covalent geometry : angle 0.59193 / 0.31 (10205) SS BOND : bond 0.00173 / 0.08 ( 2) SS BOND : angle 0.90513 / 0.38 ( 4) hydrogen bonds : bond 0.04901 / 3.36 ( 358) hydrogen bonds : angle 4.05600 / 3.03 ( 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 109 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.202 Fit side-chains REVERT: A 200 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: A 249 GLN cc_start: 0.8389 (tt0) cc_final: 0.7942 (tp-100) REVERT: A 322 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: B 19 ARG cc_start: 0.6864 (mmm-85) cc_final: 0.6388 (mmm160) REVERT: B 197 GLN cc_start: 0.6766 (mt0) cc_final: 0.6162 (tt0) REVERT: B 356 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: C 34 THR cc_start: 0.7500 (p) cc_final: 0.7290 (p) REVERT: C 217 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7841 (pp-130) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 0.4882 time to fit residues: 53.4148 Evaluate side-chains 101 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 3.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122526 restraints weight = 8212.586| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.89 r_work: 0.3166 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2396 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 : 0.551 6.290 10209 Z= 0.289 Chirality : 0.043 0.182 1176 Planarity : 0.004 0.057 1270 Dihedral : 6.326 98.400 1022 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.24 % Allowed : 16.40 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.28), residues: 903 helix: 2.45 (0.27), residues: 382 sheet: -0.28 (0.37), residues: 184 loop : -1.07 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 31 TYR 0.030 0.002 TYR A 177 PHE 0.034 0.002 PHE B 55 TRP 0.019 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 7518) covalent geometry : angle 0.55066 / 0.29 (10205) SS BOND : bond 0.00111 / 0.05 ( 2) SS BOND : angle 0.63030 / 0.27 ( 4) hydrogen bonds : bond 0.04346 / 3.00 ( 358) hydrogen bonds : angle 3.94103 / 2.95 ( 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 114 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.290 Fit side-chains REVERT: A 200 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: A 249 GLN cc_start: 0.8374 (tt0) cc_final: 0.7938 (tp-100) REVERT: B 19 ARG cc_start: 0.6803 (mmm-85) cc_final: 0.6368 (mmm160) REVERT: B 249 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8148 (mm-30) REVERT: B 356 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: C 34 THR cc_start: 0.7545 (p) cc_final: 0.7326 (p) REVERT: C 217 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7858 (pp-130) outliers start: 18 outliers final: 11 residues processed: 106 average time/residue: 0.4769 time to fit residues: 53.4498 Evaluate side-chains 105 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 3.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3796 r_free = 0.3796 target = 0.157607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122797 restraints weight = 8194.267| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.89 r_work: 0.3194 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2468 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= 0.132 Angle : 0.552 6.150 10209 Z= 0.289 Chirality : 0.043 0.183 1176 Planarity : 0.004 0.056 1270 Dihedral : 6.295 98.765 1022 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.36 % Allowed : 16.65 % Favored : 80.99 % 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: 2.51 (0.27), residues: 382 sheet: -0.30 (0.37), residues: 184 loop : -1.04 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 31 TYR 0.031 0.002 TYR A 177 PHE 0.033 0.001 PHE B 55 TRP 0.015 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7518) covalent geometry : angle 0.55223 / 0.29 (10205) SS BOND : bond 0.00138 / 0.07 ( 2) SS BOND : angle 0.57661 / 0.25 ( 4) hydrogen bonds : bond 0.04287 / 2.96 ( 358) hydrogen bonds : angle 3.90750 / 2.92 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.37 seconds wall clock time: 43 minutes 21.12 seconds (2601.12 seconds total)