Starting phenix.real_space_refine on Tue Feb 11 15:45:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lo7_23463/02_2025/7lo7_23463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lo7_23463/02_2025/7lo7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lo7_23463/02_2025/7lo7_23463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lo7_23463/02_2025/7lo7_23463.map" model { file = "/net/cci-nas-00/data/ceres_data/7lo7_23463/02_2025/7lo7_23463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lo7_23463/02_2025/7lo7_23463.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.84, per 1000 atoms: 0.95 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: 1.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.77 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: 1.50 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- 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 6306 Z= 0.542 Angle : 1.122 11.994 8578 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 : 11.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.050 0.004 TRP H 133 HIS 0.007 0.002 HIS H 241 PHE 0.040 0.004 PHE H 55 TYR 0.038 0.004 TYR Z 257 ARG 0.004 0.001 ARG H 45 *********************** 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 : 0.711 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 121 average time/residue: 0.1478 time to fit residues: 24.9426 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 : 0.654 ------------------------------------------------------------------------------- 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 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 33 optimal weight: 0.0270 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 255 GLN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN L 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.185165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161526 restraints weight = 30605.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164305 restraints weight = 24603.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.166107 restraints weight = 7652.330| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6306 Z= 0.202 Angle : 0.793 11.255 8578 Z= 0.398 Chirality : 0.046 0.138 986 Planarity : 0.006 0.094 1070 Dihedral : 6.264 54.763 869 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.62 % Allowed : 11.93 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.30), residues: 801 helix: -0.36 (0.31), residues: 294 sheet: -0.79 (0.42), residues: 164 loop : -2.06 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 133 HIS 0.006 0.001 HIS H 241 PHE 0.014 0.002 PHE Z 259 TYR 0.015 0.002 TYR Z 160 ARG 0.003 0.001 ARG H 45 *********************** 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: 9 poor density : 117 time to evaluate : 0.622 Fit side-chains REVERT: Z 109 MET cc_start: 0.8230 (mmm) cc_final: 0.7853 (mmm) REVERT: Z 125 LYS cc_start: 0.8315 (mmmm) cc_final: 0.8083 (mmmm) REVERT: Z 331 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8395 (mp) REVERT: Z 354 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7116 (t-90) REVERT: H 156 GLN cc_start: 0.6800 (tm-30) cc_final: 0.6013 (mp10) REVERT: L 60 TYR cc_start: 0.9075 (m-80) cc_final: 0.8432 (m-80) outliers start: 9 outliers final: 4 residues processed: 120 average time/residue: 0.1554 time to fit residues: 25.9524 Evaluate side-chains 110 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 331 LEU Chi-restraints excluded: chain Z residue 354 HIS 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 66 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 255 GLN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 GLN L 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.175686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.147282 restraints weight = 32188.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151057 restraints weight = 26555.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.155042 restraints weight = 7627.131| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6306 Z= 0.221 Angle : 0.741 10.170 8578 Z= 0.371 Chirality : 0.046 0.142 986 Planarity : 0.005 0.078 1070 Dihedral : 5.603 41.402 864 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 2.65 % Allowed : 16.64 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.30), residues: 801 helix: -0.04 (0.31), residues: 291 sheet: -0.76 (0.40), residues: 172 loop : -1.89 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 133 HIS 0.004 0.001 HIS H 241 PHE 0.016 0.001 PHE Z 259 TYR 0.016 0.001 TYR Z 160 ARG 0.003 0.001 ARG H 45 *********************** 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 124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.654 Fit side-chains REVERT: Z 109 MET cc_start: 0.8217 (mmm) cc_final: 0.7844 (mmm) REVERT: Z 331 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8573 (mp) REVERT: Z 354 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.7172 (t-90) REVERT: H 156 GLN cc_start: 0.6649 (tm-30) cc_final: 0.5540 (mp10) REVERT: L 60 TYR cc_start: 0.9106 (m-80) cc_final: 0.8465 (m-80) REVERT: L 190 GLN cc_start: 0.8165 (tt0) cc_final: 0.7906 (tp-100) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 0.1327 time to fit residues: 21.8878 Evaluate side-chains 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain Z residue 174 ILE Chi-restraints excluded: chain Z residue 254 PHE Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 331 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 23 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 0.0270 chunk 6 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 123 HIS H 155 ASN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.178444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.149203 restraints weight = 35811.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152277 restraints weight = 27512.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156998 restraints weight = 8049.373| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6306 Z= 0.187 Angle : 0.700 9.676 8578 Z= 0.350 Chirality : 0.044 0.137 986 Planarity : 0.005 0.072 1070 Dihedral : 5.255 38.780 864 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.09 % Allowed : 20.32 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.31), residues: 801 helix: 0.11 (0.31), residues: 298 sheet: -0.57 (0.40), residues: 171 loop : -1.81 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 133 HIS 0.015 0.002 HIS Z 123 PHE 0.015 0.001 PHE Z 258 TYR 0.014 0.001 TYR Z 160 ARG 0.003 0.000 ARG H 45 *********************** 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 133 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.630 Fit side-chains REVERT: Z 55 SER cc_start: 0.9234 (m) cc_final: 0.8856 (p) REVERT: Z 109 MET cc_start: 0.8251 (mmm) cc_final: 0.7680 (mmm) REVERT: Z 269 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6327 (tt) REVERT: Z 354 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7260 (t-90) REVERT: H 113 ARG cc_start: 0.7270 (mtp85) cc_final: 0.7029 (mtp85) REVERT: H 156 GLN cc_start: 0.6446 (tm-30) cc_final: 0.5512 (mm110) REVERT: L 60 TYR cc_start: 0.9129 (m-80) cc_final: 0.8403 (m-80) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 0.1365 time to fit residues: 24.1407 Evaluate side-chains 123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 256 ILE 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 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** L 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.175850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144815 restraints weight = 30524.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.149213 restraints weight = 26728.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.154282 restraints weight = 7724.935| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6306 Z= 0.246 Angle : 0.723 9.808 8578 Z= 0.360 Chirality : 0.045 0.147 986 Planarity : 0.005 0.071 1070 Dihedral : 5.238 37.541 864 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.09 % Allowed : 21.21 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.31), residues: 801 helix: 0.31 (0.32), residues: 287 sheet: -0.58 (0.40), residues: 171 loop : -1.76 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 133 HIS 0.019 0.002 HIS Z 123 PHE 0.019 0.002 PHE L 163 TYR 0.016 0.001 TYR Z 160 ARG 0.003 0.000 ARG H 45 *********************** 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 126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.559 Fit side-chains REVERT: Z 55 SER cc_start: 0.9236 (m) cc_final: 0.8895 (p) REVERT: Z 109 MET cc_start: 0.8241 (mmm) cc_final: 0.7595 (mmm) REVERT: Z 293 TRP cc_start: 0.6032 (t60) cc_final: 0.5793 (t-100) REVERT: Z 354 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7270 (t-90) REVERT: H 113 ARG cc_start: 0.7351 (mtp85) cc_final: 0.7083 (mtp85) REVERT: H 156 GLN cc_start: 0.6435 (tm-30) cc_final: 0.5485 (mm110) REVERT: L 60 TYR cc_start: 0.9159 (m-80) cc_final: 0.8247 (m-80) REVERT: L 193 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7919 (tmtt) outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 0.1346 time to fit residues: 22.2516 Evaluate side-chains 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 256 ILE 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 15 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.0170 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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** L 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.184782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159540 restraints weight = 32628.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162214 restraints weight = 26789.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163930 restraints weight = 8045.685| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6306 Z= 0.212 Angle : 0.705 8.915 8578 Z= 0.353 Chirality : 0.045 0.158 986 Planarity : 0.005 0.068 1070 Dihedral : 5.129 36.181 864 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.95 % Allowed : 21.65 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.31), residues: 801 helix: 0.27 (0.31), residues: 293 sheet: -0.47 (0.41), residues: 165 loop : -1.77 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 133 HIS 0.004 0.001 HIS H 241 PHE 0.015 0.001 PHE Z 16 TYR 0.015 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 *********************** 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 120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.639 Fit side-chains REVERT: Z 55 SER cc_start: 0.9207 (m) cc_final: 0.8915 (p) REVERT: Z 109 MET cc_start: 0.8152 (mmm) cc_final: 0.7478 (mmm) REVERT: Z 354 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7291 (t-90) REVERT: H 113 ARG cc_start: 0.7337 (mtp85) cc_final: 0.7118 (mtp85) REVERT: H 156 GLN cc_start: 0.6247 (tm-30) cc_final: 0.5357 (mm110) REVERT: L 193 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7895 (tmtt) outliers start: 18 outliers final: 16 residues processed: 111 average time/residue: 0.1383 time to fit residues: 21.9643 Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 118 ASP 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 256 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 190 GLN 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 = 0.184195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158894 restraints weight = 29926.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.161456 restraints weight = 27377.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.163011 restraints weight = 8292.600| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6306 Z= 0.225 Angle : 0.718 9.975 8578 Z= 0.354 Chirality : 0.045 0.154 986 Planarity : 0.005 0.068 1070 Dihedral : 5.094 35.572 864 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.39 % Allowed : 22.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.31), residues: 801 helix: 0.50 (0.32), residues: 287 sheet: -0.47 (0.41), residues: 165 loop : -1.79 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 133 HIS 0.003 0.001 HIS H 241 PHE 0.018 0.002 PHE L 163 TYR 0.016 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 *********************** 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 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.656 Fit side-chains REVERT: Z 55 SER cc_start: 0.9208 (m) cc_final: 0.8913 (p) REVERT: Z 109 MET cc_start: 0.8194 (mmm) cc_final: 0.7513 (mmm) REVERT: Z 269 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.5963 (tt) REVERT: Z 354 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7276 (t-90) REVERT: H 113 ARG cc_start: 0.7389 (mtp85) cc_final: 0.7105 (mtp85) REVERT: H 156 GLN cc_start: 0.6312 (tm-30) cc_final: 0.5412 (mm110) REVERT: L 193 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7896 (tmtt) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.1329 time to fit residues: 21.0406 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 : 0.717 ------------------------------------------------------------------------------- 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 118 ASP 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 256 ILE 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 331 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 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 71 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.0470 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 0.0370 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.188995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163836 restraints weight = 31314.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.167066 restraints weight = 26125.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170534 restraints weight = 7986.380| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6306 Z= 0.174 Angle : 0.701 10.935 8578 Z= 0.342 Chirality : 0.044 0.155 986 Planarity : 0.005 0.064 1070 Dihedral : 4.909 34.383 864 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.39 % Allowed : 22.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.31), residues: 801 helix: 0.57 (0.32), residues: 293 sheet: -0.45 (0.41), residues: 171 loop : -1.67 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 133 HIS 0.004 0.001 HIS H 241 PHE 0.016 0.001 PHE Z 258 TYR 0.014 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 *********************** 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 123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.696 Fit side-chains REVERT: Z 55 SER cc_start: 0.9237 (m) cc_final: 0.8905 (p) REVERT: Z 83 PHE cc_start: 0.8061 (m-80) cc_final: 0.7832 (m-80) REVERT: Z 354 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7374 (t-90) REVERT: H 113 ARG cc_start: 0.7305 (mtp85) cc_final: 0.7036 (mtp85) REVERT: H 156 GLN cc_start: 0.6066 (tm-30) cc_final: 0.5183 (mm110) REVERT: L 193 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7846 (tmtt) outliers start: 21 outliers final: 17 residues processed: 114 average time/residue: 0.1360 time to fit residues: 22.2547 Evaluate side-chains 120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 118 ASP Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 292 TYR Chi-restraints excluded: chain Z residue 331 LEU Chi-restraints excluded: chain Z residue 346 ILE Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain Z residue 371 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.185929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.162070 restraints weight = 25771.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164541 restraints weight = 23556.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165449 restraints weight = 7637.424| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6306 Z= 0.224 Angle : 0.728 11.964 8578 Z= 0.356 Chirality : 0.045 0.164 986 Planarity : 0.005 0.066 1070 Dihedral : 4.938 34.366 864 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.39 % Allowed : 22.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.31), residues: 801 helix: 0.58 (0.32), residues: 293 sheet: -0.46 (0.41), residues: 171 loop : -1.66 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 133 HIS 0.003 0.001 HIS H 241 PHE 0.049 0.002 PHE Z 258 TYR 0.016 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 *********************** 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 123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.643 Fit side-chains REVERT: Z 55 SER cc_start: 0.9212 (m) cc_final: 0.8934 (p) REVERT: Z 109 MET cc_start: 0.8221 (mmm) cc_final: 0.7790 (tpt) REVERT: Z 354 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7360 (t-90) REVERT: H 106 TYR cc_start: 0.8206 (m-80) cc_final: 0.7979 (m-80) REVERT: H 113 ARG cc_start: 0.7368 (mtp85) cc_final: 0.7101 (mtp85) REVERT: H 138 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: H 156 GLN cc_start: 0.6185 (tm-30) cc_final: 0.5336 (mm110) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.1297 time to fit residues: 21.5241 Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 118 ASP Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 292 TYR Chi-restraints excluded: chain Z residue 331 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 24 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: ** 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 = 0.4060 r_free = 0.4060 target = 0.184673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.159796 restraints weight = 28353.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162505 restraints weight = 25004.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.163762 restraints weight = 7814.764| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6306 Z= 0.240 Angle : 0.745 12.585 8578 Z= 0.362 Chirality : 0.045 0.163 986 Planarity : 0.005 0.066 1070 Dihedral : 5.013 35.810 864 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.31), residues: 801 helix: 0.55 (0.32), residues: 293 sheet: -0.51 (0.41), residues: 171 loop : -1.67 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 133 HIS 0.003 0.001 HIS H 241 PHE 0.047 0.002 PHE Z 258 TYR 0.017 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 ********************** 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 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.586 Fit side-chains REVERT: Z 55 SER cc_start: 0.9225 (m) cc_final: 0.8929 (p) REVERT: Z 109 MET cc_start: 0.8198 (mmm) cc_final: 0.7782 (tpt) REVERT: Z 354 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7345 (t-90) REVERT: H 106 TYR cc_start: 0.8247 (m-80) cc_final: 0.8037 (m-80) REVERT: H 138 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: H 156 GLN cc_start: 0.6205 (tm-30) cc_final: 0.5379 (mm110) outliers start: 19 outliers final: 16 residues processed: 113 average time/residue: 0.1324 time to fit residues: 21.6580 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 : 0.621 ------------------------------------------------------------------------------- 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 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 270 THR Chi-restraints excluded: chain Z residue 292 TYR Chi-restraints excluded: chain Z residue 331 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 40 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.187235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163981 restraints weight = 23822.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.166023 restraints weight = 22209.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166940 restraints weight = 7647.955| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6306 Z= 0.190 Angle : 0.728 12.823 8578 Z= 0.352 Chirality : 0.044 0.159 986 Planarity : 0.005 0.064 1070 Dihedral : 4.896 33.818 864 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.95 % Allowed : 23.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.31), residues: 801 helix: 0.60 (0.32), residues: 293 sheet: -0.44 (0.41), residues: 171 loop : -1.64 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 133 HIS 0.004 0.001 HIS H 241 PHE 0.043 0.002 PHE Z 258 TYR 0.015 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.00 seconds wall clock time: 36 minutes 53.00 seconds (2213.00 seconds total)