Starting phenix.real_space_refine on Wed Feb 4 22:44:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r0p_53487/02_2026/9r0p_53487.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r0p_53487/02_2026/9r0p_53487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r0p_53487/02_2026/9r0p_53487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r0p_53487/02_2026/9r0p_53487.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r0p_53487/02_2026/9r0p_53487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r0p_53487/02_2026/9r0p_53487.map" } resolution = 4.1 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= 0.007 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 S 25 5.16 5 C 4180 2.51 5 N 1108 2.21 5 O 1232 1.98 5 H 6651 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13196 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4840 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain: "C" Number of atoms: 4841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4841 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain: "D" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3515 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Time building chain proxies: 2.24, per 1000 atoms: 0.17 Number of scatterers: 13196 At special positions: 0 Unit cell: (74.7, 69.72, 152.72, 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 25 16.00 O 1232 8.00 N 1108 7.00 C 4180 6.00 H 6651 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 385.2 milliseconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1542 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 3 sheets defined 62.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 48 through 55 removed outlier: 4.226A pdb=" N SER B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 6.001A pdb=" N SER B 64 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 removed outlier: 4.437A pdb=" N ILE B 69 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 96 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.563A pdb=" N TYR B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 139 through 155 removed outlier: 4.544A pdb=" N LEU B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.057A pdb=" N ALA B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.617A pdb=" N ARG B 227 " --> pdb=" O ASN B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 removed outlier: 3.978A pdb=" N MET B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.437A pdb=" N ASP B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 264 removed outlier: 5.579A pdb=" N PHE B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 removed outlier: 4.707A pdb=" N LEU B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 326 removed outlier: 3.817A pdb=" N GLU B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.185A pdb=" N SER C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 removed outlier: 3.915A pdb=" N LEU C 62 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 79 Processing helix chain 'C' and resid 83 through 96 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 121 through 131 removed outlier: 3.704A pdb=" N GLU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 130 " --> pdb=" O CYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 139 through 156 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 186 through 195 Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 219 through 227 Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.819A pdb=" N LYS C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 263 through 266 removed outlier: 3.733A pdb=" N VAL C 266 " --> pdb=" O LEU C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 282 through 297 removed outlier: 3.947A pdb=" N PHE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 326 removed outlier: 3.589A pdb=" N GLU C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 removed outlier: 3.881A pdb=" N LYS D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 48 through 55 removed outlier: 4.087A pdb=" N SER D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 155 Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.510A pdb=" N GLN D 175 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 195 Processing helix chain 'D' and resid 218 through 228 removed outlier: 3.900A pdb=" N TYR D 222 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 Processing helix chain 'D' and resid 251 through 254 Processing helix chain 'D' and resid 255 through 262 Processing helix chain 'D' and resid 282 through 297 removed outlier: 3.688A pdb=" N ASN D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 326 Processing sheet with id=AA1, first strand: chain 'B' and resid 180 through 182 removed outlier: 4.303A pdb=" N VAL B 159 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU B 43 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU B 160 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU B 45 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE B 244 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU B 277 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE B 246 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS B 274 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ILE B 301 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N MET B 276 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 180 through 182 removed outlier: 6.411A pdb=" N GLU C 180 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N HIS C 204 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU C 182 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL C 159 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU C 43 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU C 160 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU C 45 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 44 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU C 247 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 46 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N HIS C 274 " --> pdb=" O LYS C 299 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE C 301 " --> pdb=" O HIS C 274 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET C 276 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR C 303 " --> pdb=" O MET C 276 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 278 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 180 through 182 removed outlier: 6.115A pdb=" N GLU D 180 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N HIS D 204 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU D 182 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL D 159 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 158 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 44 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU D 247 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL D 46 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE D 244 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU D 277 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE D 246 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG D 279 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR D 303 " --> pdb=" O MET D 276 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D 278 " --> pdb=" O TYR D 303 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 6641 1.13 - 1.30: 1172 1.30 - 1.47: 2275 1.47 - 1.65: 3185 1.65 - 1.82: 40 Bond restraints: 13313 Sorted by residual: bond pdb=" N PHE D 244 " pdb=" H PHE D 244 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG C 41 " pdb="HH11 ARG C 41 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD1 PHE C 275 " pdb=" HD1 PHE C 275 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 TYR D 307 " pdb=" HD2 TYR D 307 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 GLN C 236 " pdb="HE21 GLN C 236 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 13308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 20256 2.66 - 5.32: 3053 5.32 - 7.98: 794 7.98 - 10.64: 68 10.64 - 13.29: 10 Bond angle restraints: 24181 Sorted by residual: angle pdb=" CA PHE C 244 " pdb=" CB PHE C 244 " pdb=" CG PHE C 244 " ideal model delta sigma weight residual 113.80 122.12 -8.32 1.00e+00 1.00e+00 6.93e+01 angle pdb=" CA PHE D 244 " pdb=" CB PHE D 244 " pdb=" CG PHE D 244 " ideal model delta sigma weight residual 113.80 121.65 -7.85 1.00e+00 1.00e+00 6.16e+01 angle pdb=" CA HIS B 206 " pdb=" CB HIS B 206 " pdb=" CG HIS B 206 " ideal model delta sigma weight residual 113.80 121.04 -7.24 1.00e+00 1.00e+00 5.24e+01 angle pdb=" CA HIS C 105 " pdb=" CB HIS C 105 " pdb=" CG HIS C 105 " ideal model delta sigma weight residual 113.80 120.81 -7.01 1.00e+00 1.00e+00 4.91e+01 angle pdb=" CA PHE B 164 " pdb=" CB PHE B 164 " pdb=" CG PHE B 164 " ideal model delta sigma weight residual 113.80 120.59 -6.79 1.00e+00 1.00e+00 4.60e+01 ... (remaining 24176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5540 17.76 - 35.52: 391 35.52 - 53.28: 113 53.28 - 71.04: 116 71.04 - 88.81: 10 Dihedral angle restraints: 6170 sinusoidal: 3407 harmonic: 2763 Sorted by residual: dihedral pdb=" CA SER D 302 " pdb=" C SER D 302 " pdb=" N TYR D 303 " pdb=" CA TYR D 303 " ideal model delta harmonic sigma weight residual 180.00 146.72 33.28 0 5.00e+00 4.00e-02 4.43e+01 dihedral pdb=" CA ASP C 282 " pdb=" C ASP C 282 " pdb=" N VAL C 283 " pdb=" CA VAL C 283 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU C 200 " pdb=" C LEU C 200 " pdb=" N SER C 201 " pdb=" CA SER C 201 " ideal model delta harmonic sigma weight residual 180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 6167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 681 0.102 - 0.204: 273 0.204 - 0.305: 61 0.305 - 0.407: 9 0.407 - 0.509: 1 Chirality restraints: 1025 Sorted by residual: chirality pdb=" CA LEU D 263 " pdb=" N LEU D 263 " pdb=" C LEU D 263 " pdb=" CB LEU D 263 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.47e+00 chirality pdb=" CA PRO C 33 " pdb=" N PRO C 33 " pdb=" C PRO C 33 " pdb=" CB PRO C 33 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA PRO D 33 " pdb=" N PRO D 33 " pdb=" C PRO D 33 " pdb=" CB PRO D 33 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 1022 not shown) Planarity restraints: 1928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 209 " -0.240 2.00e-02 2.50e+03 9.98e-02 2.99e+02 pdb=" CG TYR B 209 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 209 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR B 209 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR B 209 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR B 209 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR B 209 " -0.025 2.00e-02 2.50e+03 pdb=" OH TYR B 209 " -0.189 2.00e-02 2.50e+03 pdb=" HD1 TYR B 209 " 0.057 2.00e-02 2.50e+03 pdb=" HD2 TYR B 209 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TYR B 209 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 TYR B 209 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 171 " -0.202 2.00e-02 2.50e+03 8.69e-02 2.27e+02 pdb=" CG TYR D 171 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 171 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR D 171 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR D 171 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR D 171 " 0.061 2.00e-02 2.50e+03 pdb=" CZ TYR D 171 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR D 171 " -0.168 2.00e-02 2.50e+03 pdb=" HD1 TYR D 171 " 0.025 2.00e-02 2.50e+03 pdb=" HD2 TYR D 171 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR D 171 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR D 171 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 193 " 0.196 2.00e-02 2.50e+03 6.92e-02 1.92e+02 pdb=" CG TRP D 193 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP D 193 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP D 193 " -0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP D 193 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TRP D 193 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP D 193 " -0.060 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 193 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 193 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP D 193 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 TRP D 193 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TRP D 193 " -0.061 2.00e-02 2.50e+03 pdb=" HE3 TRP D 193 " -0.060 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 193 " 0.096 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 193 " -0.015 2.00e-02 2.50e+03 pdb=" HH2 TRP D 193 " 0.061 2.00e-02 2.50e+03 ... (remaining 1925 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 771 2.19 - 2.79: 23818 2.79 - 3.39: 36356 3.39 - 4.00: 45256 4.00 - 4.60: 68092 Nonbonded interactions: 174293 Sorted by model distance: nonbonded pdb=" OE2 GLU C 169 " pdb=" HG SER C 181 " model vdw 1.582 2.450 nonbonded pdb=" OE2 GLU D 169 " pdb=" HG SER D 181 " model vdw 1.590 2.450 nonbonded pdb=" OD1 ASP D 183 " pdb=" HG1 THR D 185 " model vdw 1.620 2.450 nonbonded pdb=" HG1 THR C 229 " pdb=" OE2 GLU C 230 " model vdw 1.621 2.450 nonbonded pdb=" OD1 ASP B 183 " pdb=" HG1 THR B 185 " model vdw 1.630 2.450 ... (remaining 174288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 28 through 205 or (resid 206 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 207 through 326)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.950 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: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.480 Find NCS groups from input model: 0.130 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5551 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 : 0.013 0.043 6662 Z= 0.790 Angle : 1.994 10.018 8981 Z= 1.330 Chirality : 0.112 0.509 1025 Planarity : 0.017 0.138 1138 Dihedral : 15.134 88.805 2522 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.99 % Allowed : 5.58 % Favored : 93.43 % Rotamer: Outliers : 2.47 % Allowed : 6.72 % Favored : 90.81 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.25), residues: 807 helix: -1.72 (0.19), residues: 413 sheet: -1.39 (0.45), residues: 82 loop : -1.87 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 29 TYR 0.212 0.039 TYR B 209 PHE 0.131 0.021 PHE B 286 TRP 0.137 0.023 TRP D 193 HIS 0.010 0.003 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.01262 ( 6662) covalent geometry : angle 1.99386 ( 8981) hydrogen bonds : bond 0.19178 ( 306) hydrogen bonds : angle 7.20543 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 SER cc_start: 0.6247 (OUTLIER) cc_final: 0.5915 (p) REVERT: C 299 LYS cc_start: 0.8318 (mttt) cc_final: 0.8082 (mmtp) REVERT: D 41 ARG cc_start: 0.7292 (ptt180) cc_final: 0.6905 (mtm-85) outliers start: 18 outliers final: 8 residues processed: 154 average time/residue: 0.2031 time to fit residues: 39.3683 Evaluate side-chains 105 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 155 ASN C 241 ASN D 155 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.161597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.139455 restraints weight = 42485.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.145635 restraints weight = 24499.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.149743 restraints weight = 15758.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.152456 restraints weight = 10793.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.154359 restraints weight = 7782.214| |-----------------------------------------------------------------------------| r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6662 Z= 0.189 Angle : 0.799 10.494 8981 Z= 0.437 Chirality : 0.043 0.163 1025 Planarity : 0.005 0.057 1138 Dihedral : 8.158 36.971 868 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 0.14 % Allowed : 2.74 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.25 % 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: -1.98 (0.28), residues: 807 helix: -0.71 (0.24), residues: 417 sheet: -1.77 (0.42), residues: 108 loop : -1.82 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 324 TYR 0.034 0.003 TYR B 209 PHE 0.019 0.002 PHE B 314 TRP 0.008 0.001 TRP B 251 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6662) covalent geometry : angle 0.79884 ( 8981) hydrogen bonds : bond 0.05553 ( 306) hydrogen bonds : angle 5.56593 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 ARG cc_start: 0.7386 (ptt180) cc_final: 0.6918 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.2279 time to fit residues: 31.1871 Evaluate side-chains 85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN D 163 ASN D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.159660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.137442 restraints weight = 41546.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.143410 restraints weight = 23927.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.147467 restraints weight = 15411.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.150230 restraints weight = 10667.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.152252 restraints weight = 7764.528| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6662 Z= 0.171 Angle : 0.700 8.611 8981 Z= 0.384 Chirality : 0.041 0.169 1025 Planarity : 0.005 0.056 1138 Dihedral : 7.548 31.814 868 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.68 % Favored : 92.07 % Rotamer: Outliers : 0.14 % Allowed : 1.37 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.94 (0.28), residues: 807 helix: -0.53 (0.25), residues: 413 sheet: -2.27 (0.45), residues: 103 loop : -1.82 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 316 TYR 0.028 0.002 TYR B 209 PHE 0.017 0.002 PHE B 286 TRP 0.007 0.001 TRP D 193 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6662) covalent geometry : angle 0.70014 ( 8981) hydrogen bonds : bond 0.04923 ( 306) hydrogen bonds : angle 5.39590 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 ARG cc_start: 0.7384 (ptt180) cc_final: 0.6958 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2232 time to fit residues: 27.4276 Evaluate side-chains 82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.157699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.135228 restraints weight = 43409.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.140947 restraints weight = 25699.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.144961 restraints weight = 16930.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.147739 restraints weight = 11968.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.149759 restraints weight = 8864.390| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6662 Z= 0.177 Angle : 0.672 7.970 8981 Z= 0.367 Chirality : 0.041 0.170 1025 Planarity : 0.005 0.060 1138 Dihedral : 7.328 31.761 868 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.93 % Favored : 91.82 % Rotamer: Outliers : 0.14 % Allowed : 3.57 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.28), residues: 807 helix: -0.64 (0.24), residues: 417 sheet: -2.53 (0.51), residues: 79 loop : -1.93 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 279 TYR 0.021 0.002 TYR B 209 PHE 0.015 0.002 PHE B 314 TRP 0.006 0.001 TRP B 65 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6662) covalent geometry : angle 0.67161 ( 8981) hydrogen bonds : bond 0.04512 ( 306) hydrogen bonds : angle 5.31777 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7292 (mp0) cc_final: 0.7064 (mp0) REVERT: D 41 ARG cc_start: 0.7366 (ptt180) cc_final: 0.6983 (mtm-85) REVERT: D 298 ILE cc_start: 0.6848 (mt) cc_final: 0.6646 (mt) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.2335 time to fit residues: 26.1300 Evaluate side-chains 82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.158026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.135628 restraints weight = 43435.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.141312 restraints weight = 25685.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.145286 restraints weight = 16897.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.148102 restraints weight = 11917.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.150153 restraints weight = 8796.487| |-----------------------------------------------------------------------------| r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6662 Z= 0.163 Angle : 0.642 7.659 8981 Z= 0.351 Chirality : 0.040 0.161 1025 Planarity : 0.005 0.059 1138 Dihedral : 7.120 30.903 868 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.81 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.29), residues: 807 helix: -0.60 (0.25), residues: 416 sheet: -2.61 (0.53), residues: 71 loop : -2.01 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 233 TYR 0.019 0.002 TYR B 209 PHE 0.020 0.002 PHE C 275 TRP 0.006 0.001 TRP B 193 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6662) covalent geometry : angle 0.64164 ( 8981) hydrogen bonds : bond 0.04397 ( 306) hydrogen bonds : angle 5.28956 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7414 (mp0) cc_final: 0.7159 (mp0) REVERT: C 210 THR cc_start: 0.8806 (m) cc_final: 0.8570 (m) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2031 time to fit residues: 23.4370 Evaluate side-chains 79 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.159048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.137610 restraints weight = 41760.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.143121 restraints weight = 24607.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.147037 restraints weight = 16120.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.149757 restraints weight = 11221.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.151675 restraints weight = 8194.609| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6662 Z= 0.137 Angle : 0.599 7.232 8981 Z= 0.326 Chirality : 0.039 0.154 1025 Planarity : 0.004 0.059 1138 Dihedral : 6.779 29.577 868 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.82 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -1.83 (0.29), residues: 807 helix: -0.41 (0.25), residues: 414 sheet: -2.73 (0.52), residues: 65 loop : -1.84 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.015 0.002 TYR C 239 PHE 0.020 0.002 PHE C 275 TRP 0.016 0.001 TRP B 251 HIS 0.004 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6662) covalent geometry : angle 0.59861 ( 8981) hydrogen bonds : bond 0.04144 ( 306) hydrogen bonds : angle 5.07522 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7273 (mp0) cc_final: 0.7054 (mp0) REVERT: B 232 MET cc_start: 0.3820 (mmt) cc_final: 0.3610 (mmt) REVERT: B 313 TYR cc_start: 0.7251 (t80) cc_final: 0.6741 (t80) REVERT: D 298 ILE cc_start: 0.6067 (mt) cc_final: 0.5636 (mt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2150 time to fit residues: 24.0912 Evaluate side-chains 77 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.159122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.136940 restraints weight = 41540.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.142546 restraints weight = 24317.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.146519 restraints weight = 15931.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.149339 restraints weight = 11185.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.151310 restraints weight = 8179.151| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6662 Z= 0.142 Angle : 0.591 6.926 8981 Z= 0.322 Chirality : 0.039 0.153 1025 Planarity : 0.004 0.059 1138 Dihedral : 6.628 29.297 868 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.06 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.83 (0.29), residues: 807 helix: -0.39 (0.25), residues: 414 sheet: -2.80 (0.52), residues: 65 loop : -1.85 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 233 TYR 0.015 0.002 TYR B 209 PHE 0.020 0.002 PHE C 275 TRP 0.005 0.001 TRP B 193 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6662) covalent geometry : angle 0.59084 ( 8981) hydrogen bonds : bond 0.04012 ( 306) hydrogen bonds : angle 5.04722 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7345 (mp0) cc_final: 0.7095 (mp0) REVERT: B 313 TYR cc_start: 0.7263 (t80) cc_final: 0.6881 (t80) REVERT: D 298 ILE cc_start: 0.6045 (mt) cc_final: 0.5653 (mt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2193 time to fit residues: 23.8477 Evaluate side-chains 77 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.156436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.135365 restraints weight = 42768.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.140535 restraints weight = 25681.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.144183 restraints weight = 17154.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.146783 restraints weight = 12218.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.148597 restraints weight = 9092.240| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6662 Z= 0.174 Angle : 0.627 6.798 8981 Z= 0.345 Chirality : 0.041 0.158 1025 Planarity : 0.005 0.060 1138 Dihedral : 6.775 29.790 868 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.68 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -2.09 (0.28), residues: 807 helix: -0.53 (0.25), residues: 408 sheet: -3.04 (0.51), residues: 65 loop : -2.03 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 233 TYR 0.018 0.002 TYR B 209 PHE 0.022 0.002 PHE C 275 TRP 0.008 0.001 TRP B 193 HIS 0.005 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6662) covalent geometry : angle 0.62713 ( 8981) hydrogen bonds : bond 0.04235 ( 306) hydrogen bonds : angle 5.27647 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7414 (mp0) cc_final: 0.7083 (mp0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2088 time to fit residues: 22.6396 Evaluate side-chains 76 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.156584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.134479 restraints weight = 42760.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.139862 restraints weight = 25118.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.143655 restraints weight = 16538.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.146420 restraints weight = 11710.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.148391 restraints weight = 8663.886| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6662 Z= 0.169 Angle : 0.621 6.717 8981 Z= 0.343 Chirality : 0.040 0.154 1025 Planarity : 0.005 0.061 1138 Dihedral : 6.769 29.909 868 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.93 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -2.08 (0.28), residues: 807 helix: -0.55 (0.25), residues: 408 sheet: -2.84 (0.53), residues: 62 loop : -2.04 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 233 TYR 0.017 0.002 TYR B 209 PHE 0.022 0.002 PHE B 246 TRP 0.010 0.001 TRP D 193 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6662) covalent geometry : angle 0.62085 ( 8981) hydrogen bonds : bond 0.04206 ( 306) hydrogen bonds : angle 5.31156 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7486 (mp0) cc_final: 0.7117 (mp0) REVERT: D 276 MET cc_start: 0.7105 (ptm) cc_final: 0.6583 (ptm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1669 time to fit residues: 17.5956 Evaluate side-chains 75 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.157338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.135338 restraints weight = 42304.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.140883 restraints weight = 24806.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.144767 restraints weight = 16228.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.147485 restraints weight = 11348.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.149490 restraints weight = 8353.600| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6662 Z= 0.141 Angle : 0.592 6.488 8981 Z= 0.322 Chirality : 0.039 0.147 1025 Planarity : 0.004 0.061 1138 Dihedral : 6.551 28.598 868 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.19 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.92 (0.28), residues: 807 helix: -0.47 (0.25), residues: 415 sheet: -2.90 (0.53), residues: 62 loop : -1.88 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 233 TYR 0.014 0.002 TYR B 209 PHE 0.016 0.002 PHE C 275 TRP 0.020 0.001 TRP B 251 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6662) covalent geometry : angle 0.59160 ( 8981) hydrogen bonds : bond 0.04054 ( 306) hydrogen bonds : angle 5.20635 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7450 (mp0) cc_final: 0.7102 (mp0) REVERT: B 313 TYR cc_start: 0.7274 (t80) cc_final: 0.7010 (t80) REVERT: D 276 MET cc_start: 0.6984 (ptm) cc_final: 0.6691 (ptm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1868 time to fit residues: 19.7941 Evaluate side-chains 77 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.157411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.135856 restraints weight = 41486.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.141286 restraints weight = 24299.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.145055 restraints weight = 15900.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.147691 restraints weight = 11144.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.149499 restraints weight = 8203.846| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6662 Z= 0.145 Angle : 0.596 6.362 8981 Z= 0.327 Chirality : 0.040 0.149 1025 Planarity : 0.004 0.060 1138 Dihedral : 6.492 28.719 868 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.43 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -1.81 (0.29), residues: 807 helix: -0.40 (0.25), residues: 413 sheet: -2.92 (0.53), residues: 62 loop : -1.78 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 233 TYR 0.018 0.002 TYR D 222 PHE 0.017 0.002 PHE C 275 TRP 0.015 0.002 TRP B 65 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6662) covalent geometry : angle 0.59623 ( 8981) hydrogen bonds : bond 0.04063 ( 306) hydrogen bonds : angle 5.14220 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2367.04 seconds wall clock time: 41 minutes 4.29 seconds (2464.29 seconds total)