Starting phenix.real_space_refine on Tue Mar 3 14:36:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lo7_23463/03_2026/7lo7_23463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lo7_23463/03_2026/7lo7_23463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lo7_23463/03_2026/7lo7_23463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lo7_23463/03_2026/7lo7_23463.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lo7_23463/03_2026/7lo7_23463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lo7_23463/03_2026/7lo7_23463.map" } resolution = 3.74 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. 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 30 5.16 5 C 3995 2.51 5 N 979 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6149 Number of models: 1 Model: "" Number of chains: 3 Chain: "Z" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2751 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1764 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1755 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 232, 1755 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 1793 Chain: "L" Number of atoms: 1634 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 213, 1618 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 213, 1618 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} bond proxies already assigned to first conformer: 1634 Conformer: "C" Number of residues, atoms: 213, 1608 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved chain link angles: 4 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1634 Time building chain proxies: 2.18, per 1000 atoms: 0.35 Number of scatterers: 6149 At special positions: 0 Unit cell: (66.898, 65.819, 134.875, 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 30 16.00 O 1145 8.00 N 979 7.00 C 3995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 181 " - pdb=" SG CYS H 237 " distance=2.04 Simple disulfide: pdb=" SG CYS L 47 " - pdb=" SG CYS L 112 " distance=2.04 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG ACYS L 218 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG BCYS L 218 " distance=2.04 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CCYS L 218 " distance=2.04 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: 0.45 Conformation dependent library (CDL) restraints added in 342.1 milliseconds 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 42.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'Z' and resid 2 through 21 removed outlier: 3.756A pdb=" N PHE Z 6 " --> pdb=" O ASN Z 2 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE Z 10 " --> pdb=" O PHE Z 6 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN Z 11 " --> pdb=" O VAL Z 7 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE Z 12 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 29 Processing helix chain 'Z' and resid 36 through 53 removed outlier: 4.043A pdb=" N PHE Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Z 48 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE Z 53 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 62 removed outlier: 3.990A pdb=" N PHE Z 57 " --> pdb=" O ILE Z 53 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY Z 59 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 88 removed outlier: 3.772A pdb=" N GLY Z 88 " --> pdb=" O MET Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 120 removed outlier: 3.981A pdb=" N LEU Z 96 " --> pdb=" O SER Z 92 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET Z 109 " --> pdb=" O ALA Z 105 " (cutoff:3.500A) Proline residue: Z 110 - end of helix removed outlier: 4.068A pdb=" N ALA Z 117 " --> pdb=" O THR Z 113 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP Z 118 " --> pdb=" O GLY Z 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 151 removed outlier: 3.710A pdb=" N ILE Z 136 " --> pdb=" O MET Z 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN Z 137 " --> pdb=" O SER Z 133 " (cutoff:3.500A) Proline residue: Z 144 - end of helix removed outlier: 4.341A pdb=" N PHE Z 149 " --> pdb=" O GLY Z 145 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET Z 150 " --> pdb=" O ILE Z 146 " (cutoff:3.500A) Processing helix chain 'Z' and resid 156 through 176 removed outlier: 3.657A pdb=" N TYR Z 160 " --> pdb=" O ARG Z 156 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE Z 171 " --> pdb=" O ILE Z 167 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER Z 173 " --> pdb=" O ALA Z 169 " (cutoff:3.500A) Processing helix chain 'Z' and resid 204 through 229 removed outlier: 3.618A pdb=" N ILE Z 209 " --> pdb=" O ILE Z 205 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU Z 210 " --> pdb=" O THR Z 206 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU Z 212 " --> pdb=" O VAL Z 208 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU Z 214 " --> pdb=" O LEU Z 210 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER Z 215 " --> pdb=" O THR Z 211 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER Z 219 " --> pdb=" O SER Z 215 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA Z 220 " --> pdb=" O PHE Z 216 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU Z 224 " --> pdb=" O ALA Z 220 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER Z 226 " --> pdb=" O GLU Z 222 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU Z 227 " --> pdb=" O THR Z 223 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 256 removed outlier: 3.890A pdb=" N PHE Z 254 " --> pdb=" O PHE Z 250 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 264 removed outlier: 3.972A pdb=" N LYS Z 261 " --> pdb=" O TYR Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 266 through 288 removed outlier: 3.551A pdb=" N THR Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE Z 271 " --> pdb=" O SER Z 267 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE Z 272 " --> pdb=" O GLU Z 268 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA Z 273 " --> pdb=" O LEU Z 269 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE Z 288 " --> pdb=" O ILE Z 284 " (cutoff:3.500A) Processing helix chain 'Z' and resid 297 through 307 removed outlier: 3.709A pdb=" N VAL Z 301 " --> pdb=" O ILE Z 298 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL Z 302 " --> pdb=" O SER Z 299 " (cutoff:3.500A) Processing helix chain 'Z' and resid 309 through 321 removed outlier: 3.788A pdb=" N ALA Z 321 " --> pdb=" O PHE Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 324 through 352 removed outlier: 3.948A pdb=" N ALA Z 328 " --> pdb=" O ARG Z 324 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE Z 335 " --> pdb=" O LEU Z 331 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER Z 337 " --> pdb=" O SER Z 333 " (cutoff:3.500A) Proline residue: Z 344 - end of helix removed outlier: 4.367A pdb=" N ASP Z 352 " --> pdb=" O GLY Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 374 removed outlier: 3.864A pdb=" N TYR Z 360 " --> pdb=" O GLU Z 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET Z 361 " --> pdb=" O ALA Z 357 " (cutoff:3.500A) Processing helix chain 'Z' and resid 375 through 381 Processing helix chain 'H' and resid 54 through 57 removed outlier: 3.567A pdb=" N SER H 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 57' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 113 through 117 removed outlier: 3.924A pdb=" N THR H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 245 Processing helix chain 'L' and resid 147 through 152 removed outlier: 3.939A pdb=" N SER L 151 " --> pdb=" O SER L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 3.512A pdb=" N GLU L 211 " --> pdb=" O LYS L 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'H' and resid 72 through 78 removed outlier: 5.338A pdb=" N TRP H 73 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG H 64 " --> pdb=" O TRP H 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 118 through 120 removed outlier: 3.547A pdb=" N TYR H 120 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR H 149 " --> pdb=" O TYR H 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 161 through 165 removed outlier: 3.677A pdb=" N GLY H 180 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 183 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP H 185 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR H 217 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 236 through 238 removed outlier: 3.813A pdb=" N CYS H 237 " --> pdb=" O LYS H 250 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS H 250 " --> pdb=" O CYS H 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.561A pdb=" N THR L 29 " --> pdb=" O ARG L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 35 through 36 removed outlier: 6.015A pdb=" N LEU L 35 " --> pdb=" O GLU L 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'L' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'L' and resid 138 through 142 removed outlier: 4.011A pdb=" N VAL L 157 " --> pdb=" O PHE L 142 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL L 157 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU L 203 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU L 159 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER L 201 " --> pdb=" O LEU L 159 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN L 161 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU L 199 " --> pdb=" O ASN L 161 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE L 163 " --> pdb=" O TYR L 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER L 200 " --> pdb=" O SER L 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 168 through 174 removed outlier: 3.753A pdb=" N LYS L 169 " --> pdb=" O THR L 221 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR L 221 " --> pdb=" O LYS L 169 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU L 219 " --> pdb=" O GLN L 171 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 716 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: 0.74 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1602 1.33 - 1.45: 1287 1.45 - 1.57: 3369 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 6306 Sorted by residual: bond pdb=" CB ASP H 143 " pdb=" CG ASP H 143 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.57e+00 bond pdb=" C TRP H 133 " pdb=" O TRP H 133 " ideal model delta sigma weight residual 1.235 1.213 0.022 1.26e-02 6.30e+03 3.08e+00 bond pdb=" CG1 ILE Z 244 " pdb=" CD1 ILE Z 244 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.01e+00 bond pdb=" CB TYR Z 9 " pdb=" CG TYR Z 9 " ideal model delta sigma weight residual 1.512 1.475 0.037 2.20e-02 2.07e+03 2.86e+00 bond pdb=" CG1 ILE Z 12 " pdb=" CD1 ILE Z 12 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.68e+00 ... (remaining 6301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 8217 2.40 - 4.80: 285 4.80 - 7.20: 50 7.20 - 9.60: 19 9.60 - 11.99: 7 Bond angle restraints: 8578 Sorted by residual: angle pdb=" N THR H 201 " pdb=" CA THR H 201 " pdb=" C THR H 201 " ideal model delta sigma weight residual 114.64 107.07 7.57 1.52e+00 4.33e-01 2.48e+01 angle pdb=" C VAL H 153 " pdb=" N PHE H 154 " pdb=" CA PHE H 154 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C PHE H 187 " pdb=" N PRO H 188 " pdb=" CA PRO H 188 " ideal model delta sigma weight residual 127.00 137.27 -10.27 2.40e+00 1.74e-01 1.83e+01 angle pdb=" CA ASP H 143 " pdb=" CB ASP H 143 " pdb=" CG ASP H 143 " ideal model delta sigma weight residual 112.60 116.86 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" N ASP H 143 " pdb=" CA ASP H 143 " pdb=" C ASP H 143 " ideal model delta sigma weight residual 110.80 119.61 -8.81 2.13e+00 2.20e-01 1.71e+01 ... (remaining 8573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3236 17.97 - 35.94: 358 35.94 - 53.90: 91 53.90 - 71.87: 11 71.87 - 89.84: 7 Dihedral angle restraints: 3703 sinusoidal: 1374 harmonic: 2329 Sorted by residual: dihedral pdb=" CA LEU H 142 " pdb=" C LEU H 142 " pdb=" N ASP H 143 " pdb=" CA ASP H 143 " ideal model delta harmonic sigma weight residual 180.00 135.72 44.28 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CB CYS L 47 " pdb=" SG CYS L 47 " pdb=" SG CYS L 112 " pdb=" CB CYS L 112 " ideal model delta sinusoidal sigma weight residual -86.00 -143.13 57.13 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CA PHE Z 266 " pdb=" C PHE Z 266 " pdb=" N SER Z 267 " pdb=" CA SER Z 267 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 3700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 623 0.050 - 0.100: 272 0.100 - 0.150: 76 0.150 - 0.200: 12 0.200 - 0.250: 3 Chirality restraints: 986 Sorted by residual: chirality pdb=" CB VAL Z 22 " pdb=" CA VAL Z 22 " pdb=" CG1 VAL Z 22 " pdb=" CG2 VAL Z 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB VAL Z 365 " pdb=" CA VAL Z 365 " pdb=" CG1 VAL Z 365 " pdb=" CG2 VAL Z 365 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR H 206 " pdb=" CA THR H 206 " pdb=" OG1 THR H 206 " pdb=" CG2 THR H 206 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 983 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 133 " 0.010 2.00e-02 2.50e+03 1.93e-02 9.29e+00 pdb=" CG TRP H 133 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP H 133 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP H 133 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 133 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 133 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 133 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 133 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 133 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 133 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 126 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ALA Z 126 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA Z 126 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS Z 127 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 143 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C ASP H 143 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP H 143 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR H 144 " 0.016 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 177 2.68 - 3.23: 6145 3.23 - 3.79: 9193 3.79 - 4.34: 11663 4.34 - 4.90: 19877 Nonbonded interactions: 47055 Sorted by model distance: nonbonded pdb=" OG SER Z 236 " pdb=" OD2 ASP Z 239 " model vdw 2.123 3.040 nonbonded pdb=" O GLN H 29 " pdb=" OG SER H 51 " model vdw 2.217 3.040 nonbonded pdb=" O ALA Z 46 " pdb=" OG SER Z 50 " model vdw 2.227 3.040 nonbonded pdb=" O SER H 56 " pdb=" OG SER H 80 " model vdw 2.267 3.040 nonbonded pdb=" O THR H 84 " pdb=" OG1 THR H 84 " model vdw 2.279 3.040 ... (remaining 47050 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=0.25 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 6312 Z= 0.331 Angle : 1.122 11.994 8590 Z= 0.566 Chirality : 0.059 0.250 986 Planarity : 0.007 0.057 1070 Dihedral : 16.498 89.841 2203 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.70 % Favored : 88.18 % Rotamer: Outliers : 0.59 % Allowed : 2.21 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.56 (0.29), residues: 801 helix: -1.16 (0.29), residues: 288 sheet: -1.07 (0.43), residues: 155 loop : -2.41 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 45 TYR 0.038 0.004 TYR Z 257 PHE 0.040 0.004 PHE H 55 TRP 0.050 0.004 TRP H 133 HIS 0.007 0.002 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00816 ( 6306) covalent geometry : angle 1.12214 ( 8578) SS BOND : bond 0.00517 ( 6) SS BOND : angle 1.22469 ( 12) hydrogen bonds : bond 0.22009 ( 265) hydrogen bonds : angle 8.19966 ( 716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.210 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 121 average time/residue: 0.0574 time to fit residues: 9.9995 Evaluate side-chains 111 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ASN Chi-restraints excluded: chain L residue 171 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 9.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 255 GLN ** Z 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.153718 restraints weight = 31328.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156304 restraints weight = 26894.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.157626 restraints weight = 8448.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.161415 restraints weight = 5109.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160984 restraints weight = 3296.104| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6312 Z= 0.195 Angle : 0.834 10.262 8590 Z= 0.423 Chirality : 0.048 0.146 986 Planarity : 0.006 0.098 1070 Dihedral : 6.501 56.498 869 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 2.06 % Allowed : 12.67 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.91 (0.30), residues: 801 helix: -0.31 (0.31), residues: 288 sheet: -1.02 (0.41), residues: 168 loop : -2.18 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 45 TYR 0.023 0.002 TYR Z 29 PHE 0.021 0.002 PHE L 163 TRP 0.036 0.002 TRP H 133 HIS 0.005 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 6306) covalent geometry : angle 0.83357 ( 8578) SS BOND : bond 0.00519 ( 6) SS BOND : angle 0.80533 ( 12) hydrogen bonds : bond 0.04996 ( 265) hydrogen bonds : angle 5.92772 ( 716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.264 Fit side-chains REVERT: Z 55 SER cc_start: 0.9207 (m) cc_final: 0.8993 (p) REVERT: Z 109 MET cc_start: 0.8320 (mmm) cc_final: 0.7885 (mmm) REVERT: Z 125 LYS cc_start: 0.8364 (mmmm) cc_final: 0.8127 (mmmm) REVERT: Z 354 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.6865 (t-90) REVERT: L 60 TYR cc_start: 0.9167 (m-80) cc_final: 0.8214 (m-80) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 0.0564 time to fit residues: 9.6572 Evaluate side-chains 111 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 13 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 2 ASN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.176904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.149194 restraints weight = 28898.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152907 restraints weight = 24508.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.154938 restraints weight = 7231.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158551 restraints weight = 4432.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158339 restraints weight = 3044.923| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6312 Z= 0.134 Angle : 0.727 10.769 8590 Z= 0.364 Chirality : 0.045 0.141 986 Planarity : 0.005 0.077 1070 Dihedral : 5.489 40.606 864 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.09 % Allowed : 16.64 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.48 (0.31), residues: 801 helix: 0.03 (0.32), residues: 289 sheet: -0.71 (0.40), residues: 171 loop : -1.99 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 45 TYR 0.013 0.001 TYR Z 160 PHE 0.017 0.002 PHE Z 259 TRP 0.028 0.002 TRP H 133 HIS 0.004 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6306) covalent geometry : angle 0.72702 ( 8578) SS BOND : bond 0.00374 ( 6) SS BOND : angle 0.59832 ( 12) hydrogen bonds : bond 0.03884 ( 265) hydrogen bonds : angle 5.38641 ( 716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.207 Fit side-chains REVERT: Z 55 SER cc_start: 0.9233 (m) cc_final: 0.8977 (p) REVERT: Z 109 MET cc_start: 0.8179 (mmm) cc_final: 0.7666 (mmm) REVERT: Z 269 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6625 (tt) REVERT: Z 354 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7197 (t-90) REVERT: Z 365 VAL cc_start: 0.8323 (m) cc_final: 0.8068 (t) REVERT: H 156 GLN cc_start: 0.6479 (tm-30) cc_final: 0.5486 (mm110) REVERT: L 60 TYR cc_start: 0.9123 (m-80) cc_final: 0.8473 (m-80) outliers start: 19 outliers final: 12 residues processed: 121 average time/residue: 0.0522 time to fit residues: 9.3681 Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ASN Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 242 ILE Chi-restraints excluded: chain Z residue 254 PHE Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 2 ASN Z 51 GLN Z 123 HIS Z 255 GLN ** L 61 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 = 0.4039 r_free = 0.4039 target = 0.182853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157723 restraints weight = 19764.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161441 restraints weight = 21191.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162874 restraints weight = 7574.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.166262 restraints weight = 4950.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.166237 restraints weight = 3298.914| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6312 Z= 0.153 Angle : 0.726 9.147 8590 Z= 0.364 Chirality : 0.045 0.138 986 Planarity : 0.006 0.071 1070 Dihedral : 5.406 39.944 864 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.09 % Allowed : 20.18 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.34 (0.31), residues: 801 helix: 0.17 (0.31), residues: 288 sheet: -0.67 (0.40), residues: 171 loop : -1.89 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 45 TYR 0.016 0.002 TYR Z 160 PHE 0.018 0.002 PHE L 163 TRP 0.018 0.001 TRP H 133 HIS 0.014 0.002 HIS Z 123 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6306) covalent geometry : angle 0.72629 ( 8578) SS BOND : bond 0.00388 ( 6) SS BOND : angle 0.64349 ( 12) hydrogen bonds : bond 0.03787 ( 265) hydrogen bonds : angle 5.27493 ( 716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.227 Fit side-chains REVERT: Z 55 SER cc_start: 0.9220 (m) cc_final: 0.8919 (p) REVERT: Z 109 MET cc_start: 0.8175 (mmm) cc_final: 0.7539 (mmm) REVERT: Z 354 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7167 (t-90) REVERT: H 156 GLN cc_start: 0.6495 (tm-30) cc_final: 0.5529 (mm110) REVERT: L 60 TYR cc_start: 0.9179 (m-80) cc_final: 0.8516 (m-80) outliers start: 19 outliers final: 13 residues processed: 116 average time/residue: 0.0533 time to fit residues: 9.2053 Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 123 HIS Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 0.0070 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.178494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.150632 restraints weight = 26337.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154550 restraints weight = 24055.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156955 restraints weight = 7217.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.161482 restraints weight = 4302.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.161157 restraints weight = 2712.137| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6312 Z= 0.125 Angle : 0.693 9.231 8590 Z= 0.347 Chirality : 0.044 0.148 986 Planarity : 0.005 0.069 1070 Dihedral : 5.189 38.076 864 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.95 % Allowed : 20.77 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.22 (0.31), residues: 801 helix: 0.26 (0.32), residues: 283 sheet: -0.53 (0.40), residues: 171 loop : -1.84 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 45 TYR 0.013 0.001 TYR Z 160 PHE 0.014 0.001 PHE Z 258 TRP 0.018 0.001 TRP H 133 HIS 0.018 0.002 HIS Z 123 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6306) covalent geometry : angle 0.69365 ( 8578) SS BOND : bond 0.00325 ( 6) SS BOND : angle 0.46946 ( 12) hydrogen bonds : bond 0.03545 ( 265) hydrogen bonds : angle 5.13705 ( 716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.243 Fit side-chains REVERT: Z 55 SER cc_start: 0.9306 (m) cc_final: 0.8997 (p) REVERT: Z 109 MET cc_start: 0.8217 (mmm) cc_final: 0.7569 (mmm) REVERT: Z 269 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6143 (tt) REVERT: Z 293 TRP cc_start: 0.5755 (t60) cc_final: 0.5491 (t-100) REVERT: Z 354 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7308 (t-90) REVERT: H 156 GLN cc_start: 0.6218 (tm-30) cc_final: 0.5272 (mm110) REVERT: L 60 TYR cc_start: 0.9145 (m-80) cc_final: 0.8458 (m-80) outliers start: 18 outliers final: 13 residues processed: 115 average time/residue: 0.0572 time to fit residues: 9.6538 Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 254 PHE Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.181420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156814 restraints weight = 28359.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159277 restraints weight = 24510.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.160353 restraints weight = 7652.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163816 restraints weight = 4647.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.163342 restraints weight = 3255.758| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6312 Z= 0.180 Angle : 0.733 9.268 8590 Z= 0.368 Chirality : 0.046 0.159 986 Planarity : 0.005 0.071 1070 Dihedral : 5.295 37.321 864 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.53 % Allowed : 22.09 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.16 (0.31), residues: 801 helix: 0.41 (0.32), residues: 285 sheet: -0.53 (0.42), residues: 165 loop : -1.87 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 45 TYR 0.018 0.002 TYR Z 29 PHE 0.026 0.002 PHE L 163 TRP 0.010 0.001 TRP H 133 HIS 0.012 0.002 HIS Z 123 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 6306) covalent geometry : angle 0.73317 ( 8578) SS BOND : bond 0.00397 ( 6) SS BOND : angle 0.71343 ( 12) hydrogen bonds : bond 0.03895 ( 265) hydrogen bonds : angle 5.15005 ( 716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.220 Fit side-chains REVERT: Z 55 SER cc_start: 0.9240 (m) cc_final: 0.8983 (p) REVERT: Z 109 MET cc_start: 0.8178 (mmm) cc_final: 0.7485 (mmm) REVERT: Z 125 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7965 (tptm) REVERT: Z 269 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6033 (tt) REVERT: Z 293 TRP cc_start: 0.5971 (t60) cc_final: 0.5727 (t-100) REVERT: Z 354 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.7210 (t-90) REVERT: H 138 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: H 156 GLN cc_start: 0.6403 (tm-30) cc_final: 0.5467 (mm110) REVERT: L 60 TYR cc_start: 0.9245 (m-80) cc_final: 0.8375 (m-80) outliers start: 22 outliers final: 15 residues processed: 119 average time/residue: 0.0635 time to fit residues: 10.7711 Evaluate side-chains 126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 292 TYR Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 3 optimal weight: 0.0270 chunk 2 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 2 ASN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.185716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.160570 restraints weight = 29635.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163201 restraints weight = 26413.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164954 restraints weight = 7932.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.168441 restraints weight = 4652.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.168121 restraints weight = 3147.764| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6312 Z= 0.130 Angle : 0.712 10.681 8590 Z= 0.351 Chirality : 0.045 0.159 986 Planarity : 0.005 0.068 1070 Dihedral : 5.085 35.617 864 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.24 % Allowed : 22.53 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.02 (0.31), residues: 801 helix: 0.55 (0.32), residues: 285 sheet: -0.46 (0.41), residues: 165 loop : -1.82 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 45 TYR 0.014 0.001 TYR Z 160 PHE 0.018 0.001 PHE Z 258 TRP 0.014 0.001 TRP H 133 HIS 0.012 0.001 HIS Z 123 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6306) covalent geometry : angle 0.71189 ( 8578) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.48570 ( 12) hydrogen bonds : bond 0.03537 ( 265) hydrogen bonds : angle 5.03806 ( 716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.217 Fit side-chains REVERT: Z 55 SER cc_start: 0.9291 (m) cc_final: 0.8977 (p) REVERT: Z 125 LYS cc_start: 0.8092 (mmmm) cc_final: 0.7758 (tppp) REVERT: Z 258 PHE cc_start: 0.7483 (t80) cc_final: 0.7246 (t80) REVERT: Z 354 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7298 (t-90) REVERT: H 156 GLN cc_start: 0.6136 (tm-30) cc_final: 0.5229 (mm110) REVERT: L 60 TYR cc_start: 0.9192 (m-80) cc_final: 0.8561 (m-80) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 0.0600 time to fit residues: 10.2249 Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 272 ILE Chi-restraints excluded: chain Z residue 292 TYR Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 2 ASN Z 51 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.185897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160770 restraints weight = 31289.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163613 restraints weight = 26788.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164833 restraints weight = 7884.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.168404 restraints weight = 4649.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.168083 restraints weight = 3226.222| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6312 Z= 0.132 Angle : 0.711 11.556 8590 Z= 0.350 Chirality : 0.044 0.166 986 Planarity : 0.005 0.065 1070 Dihedral : 4.986 33.865 864 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.09 % Allowed : 22.83 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.96 (0.31), residues: 801 helix: 0.55 (0.32), residues: 291 sheet: -0.51 (0.41), residues: 171 loop : -1.74 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 45 TYR 0.014 0.001 TYR Z 160 PHE 0.018 0.001 PHE Z 258 TRP 0.011 0.001 TRP H 133 HIS 0.011 0.001 HIS Z 123 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6306) covalent geometry : angle 0.71160 ( 8578) SS BOND : bond 0.00327 ( 6) SS BOND : angle 0.52083 ( 12) hydrogen bonds : bond 0.03531 ( 265) hydrogen bonds : angle 4.95338 ( 716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.223 Fit side-chains REVERT: Z 55 SER cc_start: 0.9287 (m) cc_final: 0.8976 (p) REVERT: Z 125 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7718 (tppp) REVERT: Z 354 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7388 (t-90) REVERT: H 138 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: H 156 GLN cc_start: 0.6168 (tm-30) cc_final: 0.5266 (mm110) outliers start: 19 outliers final: 16 residues processed: 110 average time/residue: 0.0631 time to fit residues: 9.9993 Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ASN Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 292 TYR Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 2 ASN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.158721 restraints weight = 28724.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.162041 restraints weight = 26262.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.163718 restraints weight = 7788.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167512 restraints weight = 4728.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167034 restraints weight = 3187.797| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6312 Z= 0.153 Angle : 0.727 12.628 8590 Z= 0.356 Chirality : 0.045 0.166 986 Planarity : 0.005 0.066 1070 Dihedral : 5.038 35.150 864 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.09 % Allowed : 23.12 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.95 (0.31), residues: 801 helix: 0.56 (0.32), residues: 291 sheet: -0.40 (0.42), residues: 165 loop : -1.79 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 45 TYR 0.017 0.001 TYR Z 160 PHE 0.020 0.002 PHE L 163 TRP 0.009 0.001 TRP H 133 HIS 0.011 0.001 HIS Z 123 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6306) covalent geometry : angle 0.72743 ( 8578) SS BOND : bond 0.00348 ( 6) SS BOND : angle 0.60160 ( 12) hydrogen bonds : bond 0.03584 ( 265) hydrogen bonds : angle 4.94303 ( 716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.227 Fit side-chains REVERT: Z 55 SER cc_start: 0.9304 (m) cc_final: 0.9044 (p) REVERT: Z 354 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.7307 (t-90) REVERT: H 106 TYR cc_start: 0.8224 (m-80) cc_final: 0.7986 (m-80) REVERT: H 138 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: H 156 GLN cc_start: 0.6177 (tm-30) cc_final: 0.5291 (mm110) outliers start: 19 outliers final: 16 residues processed: 115 average time/residue: 0.0606 time to fit residues: 9.9071 Evaluate side-chains 123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 292 TYR Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 28 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 40 optimal weight: 0.0770 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.190154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166278 restraints weight = 29156.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168736 restraints weight = 24741.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.169900 restraints weight = 7856.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.171235 restraints weight = 5556.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.173489 restraints weight = 3740.602| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6312 Z= 0.119 Angle : 0.711 12.789 8590 Z= 0.344 Chirality : 0.044 0.157 986 Planarity : 0.005 0.063 1070 Dihedral : 4.844 33.008 864 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.36 % Allowed : 23.86 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.91 (0.31), residues: 801 helix: 0.54 (0.32), residues: 286 sheet: -0.33 (0.41), residues: 171 loop : -1.73 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 45 TYR 0.014 0.001 TYR Z 160 PHE 0.018 0.001 PHE Z 258 TRP 0.016 0.001 TRP H 133 HIS 0.011 0.001 HIS Z 123 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6306) covalent geometry : angle 0.71134 ( 8578) SS BOND : bond 0.00278 ( 6) SS BOND : angle 0.40367 ( 12) hydrogen bonds : bond 0.03332 ( 265) hydrogen bonds : angle 4.84930 ( 716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.171 Fit side-chains REVERT: Z 55 SER cc_start: 0.9299 (m) cc_final: 0.8899 (p) REVERT: Z 354 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7435 (t-90) REVERT: H 106 TYR cc_start: 0.8133 (m-80) cc_final: 0.7932 (m-80) REVERT: H 156 GLN cc_start: 0.5873 (tm-30) cc_final: 0.5007 (mm110) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 0.0539 time to fit residues: 8.8771 Evaluate side-chains 112 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 292 TYR Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.188143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163232 restraints weight = 29374.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.166024 restraints weight = 26584.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167291 restraints weight = 8040.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.171381 restraints weight = 4781.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.170715 restraints weight = 3097.548| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6312 Z= 0.132 Angle : 0.717 12.939 8590 Z= 0.349 Chirality : 0.044 0.158 986 Planarity : 0.005 0.064 1070 Dihedral : 4.854 33.205 864 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.50 % Allowed : 23.71 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.89 (0.31), residues: 801 helix: 0.55 (0.32), residues: 286 sheet: -0.33 (0.41), residues: 171 loop : -1.69 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 45 TYR 0.016 0.001 TYR Z 160 PHE 0.022 0.001 PHE Z 271 TRP 0.010 0.001 TRP H 133 HIS 0.011 0.001 HIS Z 123 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6306) covalent geometry : angle 0.71740 ( 8578) SS BOND : bond 0.00292 ( 6) SS BOND : angle 0.52430 ( 12) hydrogen bonds : bond 0.03422 ( 265) hydrogen bonds : angle 4.81818 ( 716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1056.35 seconds wall clock time: 18 minutes 56.01 seconds (1136.01 seconds total)