Starting phenix.real_space_refine on Thu Jul 2 09:31:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wf7_32461/07_2026/7wf7_32461_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wf7_32461/07_2026/7wf7_32461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wf7_32461/07_2026/7wf7_32461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wf7_32461/07_2026/7wf7_32461.map" model { file = "/net/cci-nas-00/data/ceres_data/7wf7_32461/07_2026/7wf7_32461_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wf7_32461/07_2026/7wf7_32461_neut.cif" } resolution = 3.4 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= -0.003 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 56 5.16 5 C 5207 2.51 5 N 1380 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 8136 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2189 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 5 Chain: "B" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1143 Classifications: {'peptide': 142} Link IDs: {'TRANS': 141} Chain breaks: 5 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.54, per 1000 atoms: 0.19 Number of scatterers: 8136 At special positions: 0 Unit cell: (92.4, 124.3, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 1 15.00 O 1492 8.00 N 1380 7.00 C 5207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 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: 0.44 Conformation dependent library (CDL) restraints added in 307.0 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 removed outlier: 3.755A pdb=" N ARG A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 Processing helix chain 'A' and resid 78 through 104 removed outlier: 3.634A pdb=" N TYR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 114 through 146 removed outlier: 3.638A pdb=" N MET A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 177 Processing helix chain 'A' and resid 178 through 181 removed outlier: 3.727A pdb=" N GLY A 181 " --> pdb=" O PRO A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 201 through 234 Processing helix chain 'A' and resid 254 through 280 removed outlier: 5.200A pdb=" N ILE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.757A pdb=" N LEU A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.510A pdb=" N LEU A 290 " --> pdb=" O CYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.799A pdb=" N ALA A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.558A pdb=" N TYR A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.854A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 4.008A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.609A pdb=" N CYS B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.180A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 24 Processing helix chain 'C' and resid 29 through 34 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 11 through 24 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.686A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.577A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.590A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.264A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.090A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.719A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.162A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.838A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.083A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.554A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 4.009A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.925A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.369A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 4.009A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1071 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: 1.11 Time building geometry restraints manager: 0.63 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: 2565 1.34 - 1.46: 1956 1.46 - 1.58: 3686 1.58 - 1.70: 6 1.70 - 1.83: 81 Bond restraints: 8294 Sorted by residual: bond pdb=" O1 S1P A 401 " pdb=" P22 S1P A 401 " ideal model delta sigma weight residual 1.677 1.815 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C12 S1P A 401 " pdb=" C13 S1P A 401 " ideal model delta sigma weight residual 1.528 1.601 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C10 S1P A 401 " pdb=" C11 S1P A 401 " ideal model delta sigma weight residual 1.529 1.599 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C7 S1P A 401 " pdb=" C8 S1P A 401 " ideal model delta sigma weight residual 1.532 1.601 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C6 S1P A 401 " pdb=" C7 S1P A 401 " ideal model delta sigma weight residual 1.540 1.606 -0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 10923 2.18 - 4.36: 237 4.36 - 6.54: 50 6.54 - 8.72: 5 8.72 - 10.90: 2 Bond angle restraints: 11217 Sorted by residual: angle pdb=" N PHE C 235 " pdb=" CA PHE C 235 " pdb=" C PHE C 235 " ideal model delta sigma weight residual 108.85 100.57 8.28 1.88e+00 2.83e-01 1.94e+01 angle pdb=" N TYR E 94 " pdb=" CA TYR E 94 " pdb=" C TYR E 94 " ideal model delta sigma weight residual 108.76 115.88 -7.12 1.69e+00 3.50e-01 1.78e+01 angle pdb=" C PHE C 235 " pdb=" CA PHE C 235 " pdb=" CB PHE C 235 " ideal model delta sigma weight residual 110.13 115.24 -5.11 1.34e+00 5.57e-01 1.46e+01 angle pdb=" C LEU C 70 " pdb=" CA LEU C 70 " pdb=" CB LEU C 70 " ideal model delta sigma weight residual 109.65 103.02 6.63 1.75e+00 3.27e-01 1.44e+01 angle pdb=" O1 S1P A 401 " pdb=" P22 S1P A 401 " pdb=" O25 S1P A 401 " ideal model delta sigma weight residual 105.99 95.09 10.90 3.00e+00 1.11e-01 1.32e+01 ... (remaining 11212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.86: 4808 32.86 - 65.71: 89 65.71 - 98.57: 11 98.57 - 131.42: 3 131.42 - 164.28: 1 Dihedral angle restraints: 4912 sinusoidal: 1925 harmonic: 2987 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 133.38 -40.38 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" C11 S1P A 401 " pdb=" C10 S1P A 401 " pdb=" C9 S1P A 401 " pdb=" C8 S1P A 401 " ideal model delta sinusoidal sigma weight residual 65.14 -99.14 164.28 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" N2 S1P A 401 " pdb=" C1 S1P A 401 " pdb=" C2 S1P A 401 " pdb=" O1 S1P A 401 " ideal model delta sinusoidal sigma weight residual -73.93 54.65 -128.58 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 4909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1162 0.077 - 0.154: 129 0.154 - 0.231: 6 0.231 - 0.308: 0 0.308 - 0.385: 1 Chirality restraints: 1298 Sorted by residual: chirality pdb=" C2 S1P A 401 " pdb=" C1 S1P A 401 " pdb=" C3 S1P A 401 " pdb=" N2 S1P A 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.81 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ASP C 247 " pdb=" N ASP C 247 " pdb=" C ASP C 247 " pdb=" CB ASP C 247 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 256 " pdb=" N LYS A 256 " pdb=" C LYS A 256 " pdb=" CB LYS A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1295 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 169 " -0.026 2.00e-02 2.50e+03 1.89e-02 8.94e+00 pdb=" CG TRP C 169 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 169 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 169 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 169 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.042 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO E 107 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 307 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO A 308 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.029 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2238 2.81 - 3.33: 7365 3.33 - 3.86: 12723 3.86 - 4.38: 14735 4.38 - 4.90: 25699 Nonbonded interactions: 62760 Sorted by model distance: nonbonded pdb=" OG1 THR C 143 " pdb=" OD1 ASP C 163 " model vdw 2.288 3.040 nonbonded pdb=" N GLY C 144 " pdb=" OD1 ASP C 163 " model vdw 2.295 3.120 nonbonded pdb=" O ARG C 314 " pdb=" OG SER C 331 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR C 34 " pdb=" O LEU C 300 " model vdw 2.320 3.040 nonbonded pdb=" O SER E 120 " pdb=" OG SER E 120 " model vdw 2.328 3.040 ... (remaining 62755 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.050 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 8296 Z= 0.221 Angle : 0.808 10.896 11221 Z= 0.453 Chirality : 0.047 0.385 1298 Planarity : 0.005 0.065 1388 Dihedral : 14.522 164.277 2974 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.14 (0.26), residues: 1002 helix: 0.94 (0.30), residues: 297 sheet: -0.65 (0.30), residues: 266 loop : -2.04 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 98 TYR 0.023 0.002 TYR A 198 PHE 0.017 0.002 PHE C 151 TRP 0.050 0.003 TRP C 169 HIS 0.008 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 ( 8294) covalent geometry : angle 0.80796 / 0.45 (11217) SS BOND : bond 0.01176 / 0.56 ( 2) SS BOND : angle 0.30677 / 0.18 ( 4) hydrogen bonds : bond 0.14600 / 9.38 ( 384) hydrogen bonds : angle 6.69370 / 4.86 ( 1071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 LYS cc_start: 0.4327 (mmtt) cc_final: 0.3759 (tttt) REVERT: C 158 VAL cc_start: 0.7379 (t) cc_final: 0.7134 (t) REVERT: C 279 SER cc_start: 0.5333 (p) cc_final: 0.4887 (t) REVERT: C 297 TRP cc_start: 0.7585 (m100) cc_final: 0.7144 (m100) REVERT: E 128 MET cc_start: 0.6835 (mmm) cc_final: 0.5816 (mmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0832 time to fit residues: 17.2658 Evaluate side-chains 103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 101 ASN B 347 ASN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.260860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.248292 restraints weight = 9329.022| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 0.82 r_work: 0.4432 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.4385 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8296 Z= 0.125 Angle : 0.607 7.659 11221 Z= 0.318 Chirality : 0.043 0.168 1298 Planarity : 0.004 0.044 1388 Dihedral : 9.312 173.113 1136 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.35 % Allowed : 7.54 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.23 (0.27), residues: 1002 helix: 2.06 (0.30), residues: 297 sheet: -0.26 (0.31), residues: 261 loop : -1.68 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 48 TYR 0.016 0.001 TYR A 198 PHE 0.023 0.002 PHE C 234 TRP 0.026 0.002 TRP C 169 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8294) covalent geometry : angle 0.60696 / 0.32 (11217) SS BOND : bond 0.01052 / 0.50 ( 2) SS BOND : angle 0.56134 / 0.28 ( 4) hydrogen bonds : bond 0.04672 / 2.96 ( 384) hydrogen bonds : angle 5.14366 / 3.78 ( 1071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 136 LEU cc_start: 0.7339 (tt) cc_final: 0.7120 (tp) REVERT: A 141 GLU cc_start: 0.6213 (tp30) cc_final: 0.5846 (tp30) REVERT: B 25 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: C 45 MET cc_start: 0.7040 (mpp) cc_final: 0.6808 (mpp) REVERT: C 255 LEU cc_start: 0.4340 (OUTLIER) cc_final: 0.4124 (tp) REVERT: C 289 TYR cc_start: 0.7195 (m-80) cc_final: 0.6907 (m-80) REVERT: C 297 TRP cc_start: 0.7589 (m100) cc_final: 0.6455 (t-100) REVERT: D 38 MET cc_start: 0.3932 (tmm) cc_final: 0.3272 (tmm) outliers start: 12 outliers final: 8 residues processed: 119 average time/residue: 0.0839 time to fit residues: 13.7124 Evaluate side-chains 113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 268 CYS Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 0.1980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.249587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.235940 restraints weight = 9251.854| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 0.84 r_work: 0.4358 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.4317 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8296 Z= 0.186 Angle : 0.683 9.052 11221 Z= 0.360 Chirality : 0.044 0.183 1298 Planarity : 0.005 0.043 1388 Dihedral : 8.186 144.186 1136 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.14 % Allowed : 10.80 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.32 (0.26), residues: 1002 helix: 2.16 (0.30), residues: 297 sheet: -0.55 (0.31), residues: 245 loop : -1.67 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 98 TYR 0.025 0.002 TYR C 105 PHE 0.028 0.002 PHE C 234 TRP 0.032 0.002 TRP C 169 HIS 0.007 0.002 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 8294) covalent geometry : angle 0.68328 / 0.36 (11217) SS BOND : bond 0.01391 / 0.66 ( 2) SS BOND : angle 0.67954 / 0.54 ( 4) hydrogen bonds : bond 0.05467 / 3.44 ( 384) hydrogen bonds : angle 5.22524 / 3.85 ( 1071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.312 Fit side-chains REVERT: A 141 GLU cc_start: 0.6763 (tp30) cc_final: 0.6526 (tp30) REVERT: B 189 PHE cc_start: 0.3515 (m-80) cc_final: 0.2910 (m-80) REVERT: B 349 LYS cc_start: 0.7526 (mmtt) cc_final: 0.7063 (mtmm) REVERT: C 255 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.4508 (mp) REVERT: C 289 TYR cc_start: 0.7247 (m-80) cc_final: 0.6727 (m-80) REVERT: D 38 MET cc_start: 0.4039 (tmm) cc_final: 0.3761 (tmm) REVERT: E 17 SER cc_start: 0.7616 (m) cc_final: 0.7254 (p) REVERT: E 65 LYS cc_start: 0.8010 (tptm) cc_final: 0.7612 (tttt) outliers start: 19 outliers final: 12 residues processed: 115 average time/residue: 0.0930 time to fit residues: 14.5002 Evaluate side-chains 113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 GLN ** 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 = 0.4621 r_free = 0.4621 target = 0.253773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.240099 restraints weight = 9485.630| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 0.84 r_work: 0.4383 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.4340 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8296 Z= 0.149 Angle : 0.620 9.760 11221 Z= 0.326 Chirality : 0.043 0.166 1298 Planarity : 0.004 0.045 1388 Dihedral : 7.355 127.845 1136 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.02 % Allowed : 13.05 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.16 (0.27), residues: 1002 helix: 2.31 (0.30), residues: 299 sheet: -0.58 (0.31), residues: 246 loop : -1.54 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 283 TYR 0.016 0.002 TYR C 105 PHE 0.025 0.002 PHE C 234 TRP 0.023 0.002 TRP C 169 HIS 0.007 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8294) covalent geometry : angle 0.61994 / 0.33 (11217) SS BOND : bond 0.01253 / 0.60 ( 2) SS BOND : angle 0.62217 / 0.37 ( 4) hydrogen bonds : bond 0.04831 / 3.01 ( 384) hydrogen bonds : angle 4.97092 / 3.66 ( 1071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.302 Fit side-chains REVERT: A 141 GLU cc_start: 0.6630 (tp30) cc_final: 0.6346 (tp30) REVERT: A 217 ILE cc_start: 0.5822 (OUTLIER) cc_final: 0.5415 (tt) REVERT: B 349 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7091 (mtmm) REVERT: C 101 MET cc_start: 0.7395 (mtt) cc_final: 0.7114 (mtt) REVERT: D 38 MET cc_start: 0.4038 (tmm) cc_final: 0.3800 (tmm) REVERT: E 17 SER cc_start: 0.7413 (m) cc_final: 0.7075 (p) REVERT: E 65 LYS cc_start: 0.8000 (tptm) cc_final: 0.7571 (tttt) outliers start: 18 outliers final: 14 residues processed: 109 average time/residue: 0.0966 time to fit residues: 14.3592 Evaluate side-chains 110 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4602 r_free = 0.4602 target = 0.251202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.238008 restraints weight = 9342.400| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 0.86 r_work: 0.4372 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.4337 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8296 Z= 0.190 Angle : 0.673 9.137 11221 Z= 0.355 Chirality : 0.044 0.180 1298 Planarity : 0.005 0.045 1388 Dihedral : 6.873 112.642 1136 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.37 % Allowed : 14.40 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.25 (0.27), residues: 1002 helix: 2.42 (0.29), residues: 291 sheet: -0.66 (0.31), residues: 246 loop : -1.63 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.021 0.002 TYR C 105 PHE 0.025 0.002 PHE C 234 TRP 0.025 0.002 TRP C 169 HIS 0.007 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 8294) covalent geometry : angle 0.67343 / 0.35 (11217) SS BOND : bond 0.01415 / 0.67 ( 2) SS BOND : angle 0.82803 / 0.63 ( 4) hydrogen bonds : bond 0.05421 / 3.38 ( 384) hydrogen bonds : angle 5.13449 / 3.78 ( 1071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.232 Fit side-chains REVERT: A 217 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5474 (tt) REVERT: B 53 MET cc_start: 0.4101 (pmm) cc_final: 0.2391 (pmm) REVERT: B 349 LYS cc_start: 0.7588 (mmtt) cc_final: 0.7104 (mtmm) REVERT: C 255 LEU cc_start: 0.4885 (OUTLIER) cc_final: 0.4672 (mp) REVERT: E 17 SER cc_start: 0.7884 (m) cc_final: 0.7520 (p) REVERT: E 65 LYS cc_start: 0.8003 (tptm) cc_final: 0.7796 (ttmt) REVERT: E 89 GLU cc_start: 0.6539 (tm-30) cc_final: 0.6107 (tt0) outliers start: 30 outliers final: 19 residues processed: 118 average time/residue: 0.0887 time to fit residues: 14.1905 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4589 r_free = 0.4589 target = 0.249666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.236041 restraints weight = 9297.448| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 0.89 r_work: 0.4348 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.4309 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8296 Z= 0.172 Angle : 0.651 8.875 11221 Z= 0.342 Chirality : 0.043 0.172 1298 Planarity : 0.004 0.045 1388 Dihedral : 6.519 88.159 1136 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.82 % Allowed : 14.62 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.19 (0.27), residues: 1002 helix: 2.50 (0.29), residues: 291 sheet: -0.64 (0.31), residues: 248 loop : -1.60 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 98 TYR 0.019 0.002 TYR C 105 PHE 0.020 0.002 PHE C 234 TRP 0.021 0.002 TRP C 169 HIS 0.007 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 8294) covalent geometry : angle 0.65065 / 0.34 (11217) SS BOND : bond 0.01348 / 0.64 ( 2) SS BOND : angle 0.75817 / 0.53 ( 4) hydrogen bonds : bond 0.05150 / 3.20 ( 384) hydrogen bonds : angle 5.04191 / 3.71 ( 1071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.260 Fit side-chains REVERT: A 217 ILE cc_start: 0.5875 (OUTLIER) cc_final: 0.5484 (tt) REVERT: B 53 MET cc_start: 0.4116 (pmm) cc_final: 0.2402 (pmm) REVERT: B 349 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7103 (mtmm) REVERT: C 101 MET cc_start: 0.7346 (mtt) cc_final: 0.6935 (mtt) REVERT: C 198 LEU cc_start: 0.5417 (mt) cc_final: 0.5138 (pp) REVERT: E 17 SER cc_start: 0.7790 (m) cc_final: 0.7429 (p) REVERT: E 89 GLU cc_start: 0.6404 (tm-30) cc_final: 0.5939 (tt0) outliers start: 34 outliers final: 24 residues processed: 124 average time/residue: 0.0925 time to fit residues: 15.5783 Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 GLN ** 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 = 0.4585 r_free = 0.4585 target = 0.249049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.234956 restraints weight = 9390.757| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 0.90 r_work: 0.4350 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.4309 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8296 Z= 0.165 Angle : 0.644 8.896 11221 Z= 0.336 Chirality : 0.043 0.166 1298 Planarity : 0.004 0.046 1388 Dihedral : 6.294 62.853 1136 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.60 % Allowed : 15.52 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.06 (0.27), residues: 1002 helix: 2.58 (0.29), residues: 291 sheet: -0.49 (0.32), residues: 242 loop : -1.55 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 197 TYR 0.016 0.002 TYR C 105 PHE 0.017 0.002 PHE C 234 TRP 0.020 0.002 TRP C 169 HIS 0.007 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 8294) covalent geometry : angle 0.64351 / 0.34 (11217) SS BOND : bond 0.01308 / 0.62 ( 2) SS BOND : angle 0.70916 / 0.49 ( 4) hydrogen bonds : bond 0.04974 / 3.09 ( 384) hydrogen bonds : angle 4.93862 / 3.63 ( 1071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.297 Fit side-chains REVERT: A 217 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5501 (tt) REVERT: B 53 MET cc_start: 0.4079 (pmm) cc_final: 0.2383 (pmm) REVERT: B 349 LYS cc_start: 0.7605 (mmtt) cc_final: 0.7108 (mtmm) REVERT: C 101 MET cc_start: 0.7356 (mtt) cc_final: 0.6973 (mtt) REVERT: E 17 SER cc_start: 0.7716 (m) cc_final: 0.7348 (p) outliers start: 32 outliers final: 25 residues processed: 120 average time/residue: 0.0741 time to fit residues: 12.8575 Evaluate side-chains 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 96 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 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 = 0.4593 r_free = 0.4593 target = 0.249950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.235744 restraints weight = 9323.221| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 0.90 r_work: 0.4361 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.4325 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8296 Z= 0.159 Angle : 0.633 8.708 11221 Z= 0.331 Chirality : 0.043 0.176 1298 Planarity : 0.004 0.044 1388 Dihedral : 6.303 61.841 1136 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.49 % Allowed : 15.19 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.02 (0.27), residues: 1002 helix: 2.59 (0.29), residues: 292 sheet: -0.40 (0.32), residues: 241 loop : -1.49 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 197 TYR 0.015 0.002 TYR C 105 PHE 0.019 0.002 PHE C 234 TRP 0.019 0.002 TRP C 169 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 8294) covalent geometry : angle 0.63343 / 0.33 (11217) SS BOND : bond 0.01329 / 0.63 ( 2) SS BOND : angle 0.77456 / 0.57 ( 4) hydrogen bonds : bond 0.04871 / 3.03 ( 384) hydrogen bonds : angle 4.88794 / 3.60 ( 1071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.262 Fit side-chains REVERT: A 217 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.5487 (tt) REVERT: A 237 PHE cc_start: 0.3483 (OUTLIER) cc_final: 0.2367 (m-10) REVERT: B 53 MET cc_start: 0.3597 (pmm) cc_final: 0.1948 (pmm) REVERT: B 349 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7082 (mtmm) REVERT: C 101 MET cc_start: 0.7346 (mtt) cc_final: 0.6939 (mtt) REVERT: C 198 LEU cc_start: 0.5567 (mt) cc_final: 0.5189 (pp) REVERT: E 17 SER cc_start: 0.7910 (m) cc_final: 0.7564 (p) outliers start: 31 outliers final: 24 residues processed: 118 average time/residue: 0.0744 time to fit residues: 12.3663 Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 0.0020 chunk 59 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 0.0470 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 0.0270 chunk 48 optimal weight: 0.8980 overall best weight: 0.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.261101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.252425 restraints weight = 9447.811| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 0.74 r_work: 0.4463 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.4411 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8296 Z= 0.097 Angle : 0.526 8.874 11221 Z= 0.272 Chirality : 0.040 0.156 1298 Planarity : 0.004 0.051 1388 Dihedral : 5.821 68.680 1136 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.91 % Allowed : 16.65 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.51 (0.27), residues: 1002 helix: 2.93 (0.30), residues: 294 sheet: -0.11 (0.32), residues: 254 loop : -1.19 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.015 0.001 TYR A 198 PHE 0.011 0.001 PHE A 291 TRP 0.017 0.001 TRP E 164 HIS 0.002 0.000 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.10 ( 8294) covalent geometry : angle 0.52555 / 0.27 (11217) SS BOND : bond 0.00835 / 0.40 ( 2) SS BOND : angle 0.50793 / 0.29 ( 4) hydrogen bonds : bond 0.03315 / 2.06 ( 384) hydrogen bonds : angle 4.32687 / 3.15 ( 1071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.189 Fit side-chains REVERT: B 53 MET cc_start: 0.3348 (pmm) cc_final: 0.1804 (pmm) outliers start: 17 outliers final: 13 residues processed: 116 average time/residue: 0.0795 time to fit residues: 12.9211 Evaluate side-chains 109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.0170 chunk 37 optimal weight: 0.9980 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.254844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.241290 restraints weight = 9235.713| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 0.71 r_work: 0.4288 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8296 Z= 0.114 Angle : 0.564 8.817 11221 Z= 0.291 Chirality : 0.041 0.160 1298 Planarity : 0.004 0.043 1388 Dihedral : 5.954 84.250 1136 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.57 % Allowed : 17.44 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.57 (0.27), residues: 1002 helix: 3.01 (0.29), residues: 297 sheet: -0.07 (0.31), residues: 251 loop : -1.20 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 197 TYR 0.013 0.001 TYR A 198 PHE 0.014 0.001 PHE C 234 TRP 0.031 0.002 TRP E 164 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8294) covalent geometry : angle 0.56445 / 0.29 (11217) SS BOND : bond 0.01076 / 0.51 ( 2) SS BOND : angle 0.47971 / 0.27 ( 4) hydrogen bonds : bond 0.03710 / 2.32 ( 384) hydrogen bonds : angle 4.40625 / 3.25 ( 1071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.240 Fit side-chains REVERT: A 141 GLU cc_start: 0.6819 (tp30) cc_final: 0.6438 (tp30) REVERT: B 53 MET cc_start: 0.3412 (pmm) cc_final: 0.1891 (pmm) REVERT: B 345 LYS cc_start: 0.7419 (mttt) cc_final: 0.6609 (mtmt) REVERT: B 349 LYS cc_start: 0.7588 (mmtt) cc_final: 0.6959 (mtmm) REVERT: C 289 TYR cc_start: 0.7216 (m-80) cc_final: 0.6958 (m-80) REVERT: E 59 TYR cc_start: 0.7554 (m-10) cc_final: 0.7314 (m-80) outliers start: 14 outliers final: 13 residues processed: 107 average time/residue: 0.0832 time to fit residues: 12.2851 Evaluate side-chains 109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 GLN ** 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 = 0.4615 r_free = 0.4615 target = 0.252749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.238844 restraints weight = 9272.935| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 0.72 r_work: 0.4388 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4353 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8296 Z= 0.133 Angle : 0.621 15.089 11221 Z= 0.313 Chirality : 0.041 0.157 1298 Planarity : 0.004 0.042 1388 Dihedral : 5.760 75.991 1136 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.91 % Allowed : 16.99 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.49 (0.27), residues: 1002 helix: 2.89 (0.29), residues: 299 sheet: -0.15 (0.32), residues: 245 loop : -1.20 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 197 TYR 0.013 0.002 TYR A 198 PHE 0.016 0.001 PHE C 234 TRP 0.026 0.002 TRP E 164 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8294) covalent geometry : angle 0.62145 / 0.31 (11217) SS BOND : bond 0.01285 / 0.61 ( 2) SS BOND : angle 0.62565 / 0.46 ( 4) hydrogen bonds : bond 0.04110 / 2.57 ( 384) hydrogen bonds : angle 4.53394 / 3.34 ( 1071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1860.60 seconds wall clock time: 32 minutes 34.09 seconds (1954.09 seconds total)