Starting phenix.real_space_refine on Wed Aug 5 09:30:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vus_65370/08_2026/9vus_65370.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vus_65370/08_2026/9vus_65370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vus_65370/08_2026/9vus_65370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vus_65370/08_2026/9vus_65370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vus_65370/08_2026/9vus_65370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vus_65370/08_2026/9vus_65370.map" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5729 2.51 5 N 1536 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9005 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1857 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 399 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "D" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2566 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain: "E" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1790 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2383 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 286} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'AKG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.21 Number of scatterers: 9005 At special positions: 0 Unit cell: (85.284, 119.583, 125.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1676 8.00 N 1536 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " 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: 0.70 Conformation dependent library (CDL) restraints added in 526.7 milliseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 39.4% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.664A pdb=" N ARG B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.539A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.758A pdb=" N GLN B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 216 " --> pdb=" O GLN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 274 through 279 removed outlier: 4.306A pdb=" N TYR B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 298 through 319 removed outlier: 3.694A pdb=" N ILE B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 358 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 8 through 26 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.807A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 35 Processing helix chain 'A' and resid 35 through 62 Proline residue: A 49 - end of helix removed outlier: 3.616A pdb=" N MET A 62 " --> pdb=" O TYR A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 85 removed outlier: 3.637A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 Processing helix chain 'A' and resid 102 through 137 Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 146 through 166 removed outlier: 3.667A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 191 through 207 Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 233 through 270 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 275 through 303 Proline residue: A 289 - end of helix removed outlier: 3.626A pdb=" N ALA A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing sheet with id=AA1, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.685A pdb=" N ARG B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE B 222 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 39 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASP B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 221 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE B 257 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE B 223 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN B 259 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL B 225 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 51 removed outlier: 3.578A pdb=" N ASN D 340 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.554A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.451A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 134 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.390A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 4.464A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.382A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 259 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.566A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (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 11 through 12 removed outlier: 6.788A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.677A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1320 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: 1.71 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1450 1.31 - 1.43: 2560 1.43 - 1.56: 5096 1.56 - 1.69: 0 1.69 - 1.82: 89 Bond restraints: 9195 Sorted by residual: bond pdb=" CA SER D 147 " pdb=" CB SER D 147 " ideal model delta sigma weight residual 1.531 1.475 0.055 1.59e-02 3.96e+03 1.21e+01 bond pdb=" CA SER D 316 " pdb=" CB SER D 316 " ideal model delta sigma weight residual 1.531 1.475 0.055 1.59e-02 3.96e+03 1.21e+01 bond pdb=" CA SER E 30 " pdb=" CB SER E 30 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.66e-02 3.63e+03 9.94e+00 bond pdb=" CA SER A 143 " pdb=" CB SER A 143 " ideal model delta sigma weight residual 1.531 1.478 0.052 1.72e-02 3.38e+03 9.26e+00 bond pdb=" C PRO A 167 " pdb=" O PRO A 167 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 9.09e+00 ... (remaining 9190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 12172 2.42 - 4.84: 263 4.84 - 7.26: 26 7.26 - 9.68: 2 9.68 - 12.10: 1 Bond angle restraints: 12464 Sorted by residual: angle pdb=" CA ASP A 185 " pdb=" CB ASP A 185 " pdb=" CG ASP A 185 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.00e+00 1.00e+00 4.19e+01 angle pdb=" N ILE A 144 " pdb=" CA ILE A 144 " pdb=" C ILE A 144 " ideal model delta sigma weight residual 113.07 106.74 6.33 1.36e+00 5.41e-01 2.17e+01 angle pdb=" N ASN A 179 " pdb=" CA ASN A 179 " pdb=" C ASN A 179 " ideal model delta sigma weight residual 113.23 107.54 5.69 1.24e+00 6.50e-01 2.10e+01 angle pdb=" C ASP A 185 " pdb=" CA ASP A 185 " pdb=" CB ASP A 185 " ideal model delta sigma weight residual 109.76 118.86 -9.10 1.99e+00 2.53e-01 2.09e+01 angle pdb=" CA ASP A 185 " pdb=" C ASP A 185 " pdb=" O ASP A 185 " ideal model delta sigma weight residual 121.81 116.70 5.11 1.18e+00 7.18e-01 1.87e+01 ... (remaining 12459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4633 17.23 - 34.46: 556 34.46 - 51.69: 214 51.69 - 68.92: 59 68.92 - 86.15: 12 Dihedral angle restraints: 5474 sinusoidal: 2145 harmonic: 3329 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 54.50 38.50 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" C THR D 196 " pdb=" N THR D 196 " pdb=" CA THR D 196 " pdb=" CB THR D 196 " ideal model delta harmonic sigma weight residual -122.00 -131.15 9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C ASN A 116 " pdb=" N ASN A 116 " pdb=" CA ASN A 116 " pdb=" CB ASN A 116 " ideal model delta harmonic sigma weight residual -122.60 -131.51 8.91 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 5471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1040 0.049 - 0.098: 275 0.098 - 0.147: 88 0.147 - 0.196: 12 0.196 - 0.245: 7 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA CYS E 96 " pdb=" N CYS E 96 " pdb=" C CYS E 96 " pdb=" CB CYS E 96 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA THR D 196 " pdb=" N THR D 196 " pdb=" C THR D 196 " pdb=" CB THR D 196 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN A 116 " pdb=" N ASN A 116 " pdb=" C ASN A 116 " pdb=" CB ASN A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1419 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 219 " 0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C ARG E 219 " -0.083 2.00e-02 2.50e+03 pdb=" O ARG E 219 " 0.031 2.00e-02 2.50e+03 pdb=" N LEU E 220 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO E 75 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 44 " 0.014 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C HIS C 44 " -0.046 2.00e-02 2.50e+03 pdb=" O HIS C 44 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA C 45 " 0.016 2.00e-02 2.50e+03 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1629 2.77 - 3.30: 8415 3.30 - 3.83: 15867 3.83 - 4.37: 19202 4.37 - 4.90: 32613 Nonbonded interactions: 77726 Sorted by model distance: nonbonded pdb=" O GLY E 112 " pdb=" OG SER E 185 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 176 " model vdw 2.239 3.040 nonbonded pdb=" O CYS B 332 " pdb=" OG SER B 333 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR D 274 " pdb=" O VAL D 315 " model vdw 2.298 3.040 nonbonded pdb=" OG SER D 161 " pdb=" OD2 ASP D 163 " model vdw 2.304 3.040 ... (remaining 77721 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.006 0.057 9199 Z= 0.337 Angle : 0.797 12.104 12472 Z= 0.522 Chirality : 0.051 0.245 1422 Planarity : 0.005 0.084 1575 Dihedral : 18.123 86.155 3310 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 2.81 % Allowed : 27.21 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.46 (0.25), residues: 1125 helix: 1.33 (0.26), residues: 405 sheet: 0.10 (0.30), residues: 291 loop : -0.42 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 268 TYR 0.017 0.002 TYR B 358 PHE 0.010 0.002 PHE D 151 TRP 0.011 0.001 TRP D 339 HIS 0.005 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.34 ( 9195) covalent geometry : angle 0.79658 / 0.52 (12464) SS BOND : bond 0.01041 / 0.52 ( 4) SS BOND : angle 1.49959 / 0.84 ( 8) hydrogen bonds : bond 0.16873 / 10.89 ( 463) hydrogen bonds : angle 7.01351 / 5.01 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.385 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 219 average time/residue: 0.5737 time to fit residues: 133.5024 Evaluate side-chains 203 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 181 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN B 216 ASN B 238 ASN C 24 ASN D 13 GLN D 44 GLN D 293 ASN D 295 ASN E 143 GLN A 91 HIS A 278 ASN A 294 ASN A 308 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114335 restraints weight = 12046.708| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.44 r_work: 0.3490 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9199 Z= 0.156 Angle : 0.522 5.930 12472 Z= 0.282 Chirality : 0.042 0.179 1422 Planarity : 0.005 0.053 1575 Dihedral : 7.112 65.073 1272 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.32 % Allowed : 25.20 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.07 (0.25), residues: 1125 helix: 2.05 (0.25), residues: 413 sheet: 0.43 (0.30), residues: 281 loop : -0.36 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 268 TYR 0.019 0.002 TYR A 58 PHE 0.012 0.001 PHE A 113 TRP 0.017 0.002 TRP D 82 HIS 0.004 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 9195) covalent geometry : angle 0.52108 / 0.28 (12464) SS BOND : bond 0.00687 / 0.34 ( 4) SS BOND : angle 1.48571 / 0.79 ( 8) hydrogen bonds : bond 0.04765 / 2.99 ( 463) hydrogen bonds : angle 5.12215 / 3.65 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.369 Fit side-chains REVERT: D 59 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: E 115 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7099 (m) outliers start: 43 outliers final: 27 residues processed: 215 average time/residue: 0.5336 time to fit residues: 122.2357 Evaluate side-chains 213 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 315 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 75 optimal weight: 0.0070 chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 82 optimal weight: 0.0970 chunk 111 optimal weight: 0.3980 overall best weight: 0.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN B 231 ASN B 238 ASN D 155 ASN D 293 ASN E 143 GLN A 28 ASN A 281 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.122687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111811 restraints weight = 12166.722| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.44 r_work: 0.3530 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9199 Z= 0.098 Angle : 0.463 7.490 12472 Z= 0.247 Chirality : 0.040 0.140 1422 Planarity : 0.004 0.050 1575 Dihedral : 6.293 58.599 1262 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.12 % Allowed : 25.90 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.29 (0.25), residues: 1125 helix: 2.37 (0.25), residues: 412 sheet: 0.42 (0.30), residues: 281 loop : -0.29 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 309 TYR 0.017 0.001 TYR E 191 PHE 0.009 0.001 PHE A 115 TRP 0.017 0.001 TRP D 82 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 9195) covalent geometry : angle 0.46248 / 0.25 (12464) SS BOND : bond 0.00530 / 0.27 ( 4) SS BOND : angle 1.02887 / 0.55 ( 8) hydrogen bonds : bond 0.03868 / 2.43 ( 463) hydrogen bonds : angle 4.71062 / 3.36 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: B 199 PHE cc_start: 0.8320 (m-80) cc_final: 0.7997 (m-80) REVERT: D 59 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: D 258 ASP cc_start: 0.7508 (t0) cc_final: 0.7076 (t0) REVERT: E 115 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7080 (m) outliers start: 41 outliers final: 19 residues processed: 226 average time/residue: 0.5267 time to fit residues: 126.8900 Evaluate side-chains 219 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 181 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN B 238 ASN D 155 ASN D 230 ASN D 239 ASN D 293 ASN A 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109224 restraints weight = 12221.568| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.45 r_work: 0.3494 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9199 Z= 0.166 Angle : 0.508 5.866 12472 Z= 0.271 Chirality : 0.042 0.176 1422 Planarity : 0.004 0.053 1575 Dihedral : 6.329 58.160 1261 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.72 % Allowed : 25.60 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.36 (0.25), residues: 1125 helix: 2.45 (0.25), residues: 406 sheet: 0.43 (0.29), residues: 281 loop : -0.21 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 309 TYR 0.021 0.002 TYR A 58 PHE 0.014 0.002 PHE A 113 TRP 0.014 0.001 TRP D 82 HIS 0.004 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9195) covalent geometry : angle 0.50684 / 0.27 (12464) SS BOND : bond 0.01045 / 0.52 ( 4) SS BOND : angle 1.56626 / 0.82 ( 8) hydrogen bonds : bond 0.04368 / 2.72 ( 463) hydrogen bonds : angle 4.74075 / 3.39 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 231 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7362 (m-40) REVERT: B 267 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8013 (ttmt) REVERT: B 309 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7623 (ttp80) REVERT: D 59 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: D 197 ARG cc_start: 0.7864 (mmt180) cc_final: 0.7192 (mmt-90) REVERT: D 214 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7608 (mtt180) REVERT: E 115 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7122 (m) outliers start: 47 outliers final: 29 residues processed: 215 average time/residue: 0.5496 time to fit residues: 125.4434 Evaluate side-chains 220 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 272 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 52 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 216 ASN B 238 ASN D 155 ASN D 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.120662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109473 restraints weight = 12166.113| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.49 r_work: 0.3496 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9199 Z= 0.142 Angle : 0.491 5.809 12472 Z= 0.263 Chirality : 0.042 0.184 1422 Planarity : 0.004 0.056 1575 Dihedral : 6.263 59.809 1261 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.42 % Allowed : 26.61 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.33 (0.25), residues: 1125 helix: 2.42 (0.25), residues: 406 sheet: 0.43 (0.29), residues: 281 loop : -0.24 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 19 TYR 0.015 0.001 TYR E 191 PHE 0.012 0.001 PHE A 113 TRP 0.014 0.001 TRP D 82 HIS 0.003 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9195) covalent geometry : angle 0.49008 / 0.26 (12464) SS BOND : bond 0.00836 / 0.42 ( 4) SS BOND : angle 1.45219 / 0.77 ( 8) hydrogen bonds : bond 0.04145 / 2.58 ( 463) hydrogen bonds : angle 4.67935 / 3.33 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.226 Fit side-chains REVERT: B 199 PHE cc_start: 0.8372 (m-80) cc_final: 0.7978 (m-80) REVERT: B 267 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8010 (ttmt) REVERT: B 309 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7644 (ttp80) REVERT: D 59 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: D 155 ASN cc_start: 0.8447 (t0) cc_final: 0.8221 (t0) REVERT: D 197 ARG cc_start: 0.7875 (mmt180) cc_final: 0.7173 (mmt-90) REVERT: D 214 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7601 (mtt180) REVERT: D 258 ASP cc_start: 0.7532 (t0) cc_final: 0.7144 (t0) REVERT: E 115 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7095 (m) outliers start: 44 outliers final: 26 residues processed: 209 average time/residue: 0.5344 time to fit residues: 118.8836 Evaluate side-chains 215 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 315 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN B 238 ASN D 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108839 restraints weight = 12172.945| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.44 r_work: 0.3490 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9199 Z= 0.174 Angle : 0.521 9.435 12472 Z= 0.274 Chirality : 0.043 0.186 1422 Planarity : 0.004 0.055 1575 Dihedral : 5.979 59.380 1257 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.32 % Allowed : 26.41 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.33 (0.25), residues: 1125 helix: 2.38 (0.25), residues: 406 sheet: 0.45 (0.30), residues: 281 loop : -0.21 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 261 TYR 0.022 0.002 TYR A 58 PHE 0.014 0.001 PHE A 113 TRP 0.013 0.001 TRP D 82 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 9195) covalent geometry : angle 0.51923 / 0.27 (12464) SS BOND : bond 0.00833 / 0.42 ( 4) SS BOND : angle 1.72888 / 0.91 ( 8) hydrogen bonds : bond 0.04318 / 2.68 ( 463) hydrogen bonds : angle 4.71578 / 3.36 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 199 PHE cc_start: 0.8368 (m-80) cc_final: 0.7813 (m-80) REVERT: B 309 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7653 (ttp80) REVERT: D 59 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: D 197 ARG cc_start: 0.7832 (mmt180) cc_final: 0.7170 (mmt-90) REVERT: D 214 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7561 (mtt180) REVERT: E 83 MET cc_start: 0.8599 (mtm) cc_final: 0.8280 (mtp) outliers start: 43 outliers final: 26 residues processed: 214 average time/residue: 0.5923 time to fit residues: 134.6555 Evaluate side-chains 214 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 315 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN B 238 ASN D 237 ASN D 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108994 restraints weight = 12206.388| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.50 r_work: 0.3485 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9199 Z= 0.163 Angle : 0.531 9.347 12472 Z= 0.278 Chirality : 0.043 0.208 1422 Planarity : 0.004 0.056 1575 Dihedral : 5.583 58.452 1255 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.61 % Allowed : 26.61 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.39 (0.25), residues: 1125 helix: 2.50 (0.25), residues: 400 sheet: 0.47 (0.29), residues: 282 loop : -0.20 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.018 0.002 TYR E 191 PHE 0.013 0.001 PHE A 113 TRP 0.014 0.001 TRP D 82 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 9195) covalent geometry : angle 0.52980 / 0.28 (12464) SS BOND : bond 0.01097 / 0.55 ( 4) SS BOND : angle 1.73710 / 0.87 ( 8) hydrogen bonds : bond 0.04275 / 2.63 ( 463) hydrogen bonds : angle 4.69114 / 3.35 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.336 Fit side-chains REVERT: B 199 PHE cc_start: 0.8366 (m-80) cc_final: 0.8021 (m-80) REVERT: B 309 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7644 (ttp80) REVERT: D 59 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: D 155 ASN cc_start: 0.8443 (t0) cc_final: 0.8216 (t0) REVERT: D 197 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7183 (mmt-90) REVERT: D 214 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7540 (mtt180) REVERT: D 258 ASP cc_start: 0.7532 (t0) cc_final: 0.7169 (t0) REVERT: E 83 MET cc_start: 0.8581 (mtm) cc_final: 0.8282 (mtp) outliers start: 36 outliers final: 22 residues processed: 204 average time/residue: 0.5578 time to fit residues: 120.9024 Evaluate side-chains 208 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 315 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 43 optimal weight: 0.0670 chunk 84 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN B 238 ASN D 230 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.120507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109535 restraints weight = 12159.199| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.43 r_work: 0.3497 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9199 Z= 0.157 Angle : 0.526 9.112 12472 Z= 0.275 Chirality : 0.042 0.188 1422 Planarity : 0.004 0.055 1575 Dihedral : 5.395 57.770 1255 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.01 % Allowed : 27.31 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.43 (0.25), residues: 1125 helix: 2.53 (0.25), residues: 400 sheet: 0.46 (0.29), residues: 284 loop : -0.16 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 268 TYR 0.025 0.002 TYR A 58 PHE 0.013 0.001 PHE A 113 TRP 0.014 0.001 TRP D 82 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 9195) covalent geometry : angle 0.52541 / 0.27 (12464) SS BOND : bond 0.00991 / 0.49 ( 4) SS BOND : angle 1.41669 / 0.72 ( 8) hydrogen bonds : bond 0.04227 / 2.62 ( 463) hydrogen bonds : angle 4.67312 / 3.33 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.224 Fit side-chains REVERT: B 199 PHE cc_start: 0.8359 (m-80) cc_final: 0.7986 (m-80) REVERT: B 309 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7653 (ttp80) REVERT: D 59 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: D 197 ARG cc_start: 0.7880 (mmt180) cc_final: 0.7190 (mmt-90) REVERT: D 214 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7569 (mtt180) REVERT: D 258 ASP cc_start: 0.7515 (t0) cc_final: 0.7134 (t0) REVERT: E 90 ASP cc_start: 0.7775 (m-30) cc_final: 0.7513 (m-30) outliers start: 30 outliers final: 23 residues processed: 204 average time/residue: 0.5205 time to fit residues: 112.5218 Evaluate side-chains 210 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 315 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN B 238 ASN D 237 ASN E 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.119156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.107964 restraints weight = 12129.931| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.48 r_work: 0.3475 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9199 Z= 0.228 Angle : 0.571 9.558 12472 Z= 0.299 Chirality : 0.045 0.246 1422 Planarity : 0.004 0.057 1575 Dihedral : 5.511 58.031 1254 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.11 % Allowed : 27.31 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.29 (0.25), residues: 1125 helix: 2.30 (0.25), residues: 400 sheet: 0.43 (0.29), residues: 285 loop : -0.15 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 268 TYR 0.015 0.002 TYR E 191 PHE 0.017 0.002 PHE A 113 TRP 0.012 0.002 TRP D 82 HIS 0.003 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 ( 9195) covalent geometry : angle 0.56940 / 0.30 (12464) SS BOND : bond 0.01214 / 0.61 ( 4) SS BOND : angle 1.66885 / 0.87 ( 8) hydrogen bonds : bond 0.04617 / 2.86 ( 463) hydrogen bonds : angle 4.81571 / 3.44 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.221 Fit side-chains REVERT: B 199 PHE cc_start: 0.8378 (m-80) cc_final: 0.7979 (m-80) REVERT: B 309 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7710 (ttp80) REVERT: D 59 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: D 197 ARG cc_start: 0.7875 (mmt180) cc_final: 0.7200 (mmt-90) REVERT: D 214 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7555 (mtt180) REVERT: E 53 SER cc_start: 0.7712 (p) cc_final: 0.7462 (t) REVERT: E 90 ASP cc_start: 0.7797 (m-30) cc_final: 0.7530 (m-30) outliers start: 31 outliers final: 21 residues processed: 203 average time/residue: 0.4983 time to fit residues: 107.3305 Evaluate side-chains 206 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 315 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 107 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN B 238 ASN D 237 ASN D 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108999 restraints weight = 12098.727| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.43 r_work: 0.3491 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9199 Z= 0.184 Angle : 0.552 9.152 12472 Z= 0.288 Chirality : 0.044 0.244 1422 Planarity : 0.004 0.055 1575 Dihedral : 5.376 57.353 1254 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.61 % Allowed : 28.41 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.31 (0.25), residues: 1125 helix: 2.39 (0.25), residues: 399 sheet: 0.41 (0.29), residues: 285 loop : -0.19 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 268 TYR 0.015 0.002 TYR E 191 PHE 0.014 0.001 PHE A 113 TRP 0.014 0.002 TRP D 82 HIS 0.003 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 9195) covalent geometry : angle 0.55037 / 0.29 (12464) SS BOND : bond 0.01071 / 0.54 ( 4) SS BOND : angle 1.50223 / 0.79 ( 8) hydrogen bonds : bond 0.04395 / 2.72 ( 463) hydrogen bonds : angle 4.76086 / 3.39 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.288 Fit side-chains REVERT: B 199 PHE cc_start: 0.8362 (m-80) cc_final: 0.7953 (m-80) REVERT: B 309 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7671 (ttp80) REVERT: D 59 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: D 197 ARG cc_start: 0.7846 (mmt180) cc_final: 0.6742 (mmt-90) REVERT: D 214 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7467 (mtt180) REVERT: D 258 ASP cc_start: 0.7522 (t0) cc_final: 0.7199 (t0) REVERT: E 53 SER cc_start: 0.7685 (p) cc_final: 0.7441 (t) outliers start: 26 outliers final: 20 residues processed: 201 average time/residue: 0.4715 time to fit residues: 100.9485 Evaluate side-chains 204 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 315 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 110 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN B 238 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110299 restraints weight = 11996.098| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.47 r_work: 0.3507 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9199 Z= 0.118 Angle : 0.508 8.708 12472 Z= 0.266 Chirality : 0.041 0.224 1422 Planarity : 0.004 0.055 1575 Dihedral : 5.114 56.096 1254 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.21 % Allowed : 29.32 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.38 (0.25), residues: 1125 helix: 2.47 (0.25), residues: 406 sheet: 0.41 (0.29), residues: 285 loop : -0.17 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 19 TYR 0.013 0.001 TYR E 191 PHE 0.010 0.001 PHE A 113 TRP 0.015 0.001 TRP D 82 HIS 0.002 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9195) covalent geometry : angle 0.50691 / 0.27 (12464) SS BOND : bond 0.00787 / 0.39 ( 4) SS BOND : angle 1.15642 / 0.60 ( 8) hydrogen bonds : bond 0.03960 / 2.46 ( 463) hydrogen bonds : angle 4.61781 / 3.27 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3719.35 seconds wall clock time: 63 minutes 58.68 seconds (3838.68 seconds total)